Re: [galaxy-user] Cuffdiff question
Hi Clare We just ran into a similar issue about a week ago and were debugging with the authors of cuffdiff Apparently there are issues with the -b parameter - were you using this in cufflinks? If yes - this may be the cause - we switched the order of the replicates and the values changed; as did PCA's of the samples, etc They are working on this issue for an upcoming version of cufflinks. I am interested in knowing whether this was indeed your problem or were you using a pipeline that does not include cufflinks? Good luck, Noa On 14/11/2013 13:13, clare Hardman wrote: Hello, Could you please advise me on this probably naive question. When I compare sample A and sample B by Ciffdiff and then separately compare Sample A to Sample C by Cuffdiff too, should the FMPK value be the same for A in both tests? At the moment mine does not seem to be! Best wishes Clare ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Map with BWA for Illumina is hung
Was this ever resolved? I am in the same situation for 3 days now. I tried to rerun as well - stays marked grey forever. THanks Noa On 30/04/2013 17:36, Casey,Richard wrote: Hi, when we try using Map with BWA for Illumina on the public server, it never starts running and sits in a queued state forever. We have jobs that have been queued for more than 5 days. Any ideas on why these jobs never start? --- Richard Casey, PhD CSU 970-492-4127 970-980-5975 richard.ca...@colostate.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Why don't we get FPKMs from this gene?
i will look later there is a wellknown bug in cufflinks i solved it once and it took me forever and will prob take me forever to remember... n On 14/02/2013 11:48, Dikla Aharonovich wrote: Hello, We are using BAM to map Illumina reads to a bacterial genome, followed by Cufflinks o get the FPKMs. We have come across many genes for which we get FPKM=0 (using both gene and transcript _expression_) even though there are reads mapping to these gene IDs (e.g. the region between the dashed lines in the attached screenshot). Can anyone suggest a reason/fix for this? Thanks Dikla ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Help!!! cuffdiff log2 value
I think the sign is to show if it is x-fold more than the first condition (+) or x-fold less than the first condition (-). A regular fold would give you values from 1-whatever if sample 2 is more than sample 1, and a fraction (0-1) if sample 1 is expressed more than sample 2. The log lets you get both on the same scale, so that 2 means (on log2 scale) four-fold upregulated, and -2 means four-fold downregulated. FPKM x FPKM y y/x log(y/x) 1 2 2 1 1 0.5 0.5 -1 On 10/05/2012 19:00, Jennifer Jackson wrote: Hi Jiwen, As far as I know, this is possible. The CuffDiff log2 value is defined here: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff 7 FPKMx 8.01089 FPKM of the gene in sample x 8 FPKMy 8.551545 FPKM of the gene in sample y 9 log2(FPKMy/FPKMx) 0.06531 The (base 2) log of the fold change y/x And log(2) in general (including a graph, which can help with visualizing) is described here (although the web is full if similar): http://en.wikipedia.org/wiki/Logarithm I can see that this same Q on seqanswers.com recieved pretty much the same answer (in brief! http://seqanswers.com/forums/showthread.php?t=19558), so I think you are safe using the data as it as generated. Taking a look at the inputs would be advised if the results were unexpected. If you do still have concerns about the log(2) calculation, asking the tool authors directly (if you have't done so already) at tophat.cuffli...@gmail.com is always an option, to tripple check. Best, Jen Galaxy team On 4/26/12 7:48 AM, 杨继文 wrote: Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expressed transcrpts or genes. As far as I know, log2 value = fold change. However, there are minus values. Is this possible?? log2 value can not be minus. Did I miss something?? Looking forward to your help. Thanks in advance. Best Jiwen 网易Lofter，专注兴趣，分享创作！ http://www.lofter.com ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] velvetoptimizer on galaxy toolshed
Hi I want to use VelvetOptimizer, and saw that it is availbale on the galaxy toolshed. I have never used this and have no idea how to- do I download it or is this something that works with the glaaxy GUI? What do I need on my computer to run it? Or is this something for linux? Thanks Noa ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Cufflinks related problem
Hi Ateeq I am running either bowtie and then cufflinks or tophat and then cufflinks. With bacteria there is not much of a reason to use tophat since you arent expecting alternative splicing. If you DO decide to do tophat and then cufflinks, play with the intron size parameters. For bowtie I have been using a genome in FASTA format. When you then go to cufflinks you can give it your reference gene annotation in gtf format so it recognizes the genes that were aligned to the genome. Hope that helps Noa On 22/02/2012 11:32, Ateequr Rehman wrote: Dear Bomba I am bit confused , Are you running bowtie --- tophat Cufflink For bowtie run you are using reference genome annotation in gff3 format I am curremntly totally unable to figure it out correctly, how i should analyse my RNA seq data Best Ateeq From: Noa Sher noa.s...@gmail.com To: Bomba Dam bomba@visva-bharati.ac.in Cc: galaxy-user@lists.bx.psu.edu Sent: Wednesday, February 22, 2012 7:28 AM Subject: Re: [galaxy-user] Cufflinks related problem Hi Bomba I cant know for sure without seeing your files but I originally had the same problem and it ended up being because the way the genome was named in the fasta genome file was not the same as the way it was named in column 1 of my gtf file. I would check that first. Also- with bacteria you dont want to run cufflinks with default parameters- use the galaxy browser to check how your data looks after tophat and you will most likely see very strange gene-spanning introns. Change the max intron size to 1000-1500 and the min distnace to 101-5nt and you should get results that make much more sense. Good luck Noa On 22/02/2012 00:12, Bomba Dam wrote: Dear Noa, Can you please tell me the parameters that I should keep while mapping bacterial transcripts using cuffkins. I have kept the default parameters as in Cufflinks and used my custom genome annotation in gff3 format. The cufflinks seems to work Ok but all the FPKM values in these files are zero. As suggested by other users I have checked the correctness of my GFF3 files. The corresponding fasta file was used for mapping the transcripts using Bowtie. Are there any special trick for mapping bacterial transcriptome. regards, Bomba ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Using galaxy for Bacterial RNA-seq
Hi Bomba I have been recently struggling with the same issue (RNA-Seq on a bacteria; no programming experience). I was in touch with the authors of the tophat-cufflinks suite and they all suggested that given that bacteria have little or no introns, you can do bowtie followed by cufflinks and skip the tophat. Alternatively, if you do decide to do tophat and then cufflinks, make SURE to change the intron size parameters, otherwise you will get a mess. I used min intron distance 10bp, max size 1000bp. If you just want to do comparative work you can do bowtie and then cuffdiff directly. Look at your data with the Galaxy genome browser after you run tophat or bowtie to make sure it looks OK. (I found it easier to convert bowtie data from SAM to BAM file and then to view it). One thing I havent fully looked into is what happens at the ends of the mapping (since bowtie assumes linear chromosomes and not circularized, so just be aware of that difference as not all reads will align properly at the ends). Feel free to contact me if you need more help - I am definitely not an expert but have been struggling through doing RNA-Seq on galaxy for the past month or so, so may be able to help with some things. Make sure you use matching gtf reference annotation (if you have this) and genome! Good luck! noa On 16/02/2012 20:01, Jeremy Goecks wrote: Bomba, I'm not familiar enough with bacterial/prokaryotic transcriptomes to suggest a possible workflow. You might try the standard Tophat-Cufflinks-Cuffcompare/merge-Cuffdiff workflow and see whether you get meaningful results; Tophat runs Bowtie internally, so there's no reason to run Bowtie separately unless there are Bowtie-specific parameters that you need to modify. I've had very little experience with PALMapper and can't speak to its efficacy, either for eukaryotic or prokaryotic transcriptome analyses. Finally, I've cc'd the galaxy-user mailing list. Using this list is the best way to reach the Galaxy user community and get in touch with someone that has used Galaxy to analyze bacterial transcriptomes. Good luck, J. On Feb 16, 2012, at 9:17 AM, Bomba Dam wrote: Dear Dr. Goecks, I am working as a post-doctoral fellow in MPI Marburg, Germany. We am trying to understand the differential _expression_ of genes in a methanotrophic bacterium under different growth conditions. We are sequencing the transcriptome using Illumina Hiseq. As I dont have expertise in programming languages, I found the Galaxy interface very user-friendly for doing such transcriptome analysis. However, I could not find a step wise protocol\workflow for mapping bacterial RNA-seq against the reference genome (we have the completely sequenced genome of our model organism). I have found a detailed step by step workflow for RNA-seq analysis from the University of Alabama web-site (uab.edu). However, it refers to the eukaryotic system. Most examples provided and used for analysis are from eukaryotic systems. I am a bit confused weather the same workflow will also work well for bacterial systems as there are no splicing events or I should make some modifications. Can you kindly suggest me which workflow should I follow for mapping the bacterial reads (Bowtie, Tophat or PALMapper) and subsequent quantification steps. I want some guidance in this regard. With kind regards, Bomba Dam -- Dr. BOMBA DAM Alexander von Humboldt Postdoctoral Research Fellow Max-Planck-Institut fr terrestrische Mikrobiologie Karl-von-Frisch-Strae 10 D-35043 Marburg, Germany E mail: bomba@mpi-marburg.mpg.de PHONE: +49 176 321 321 75 (Mobile); +49 6421 178 721 (LAB); +49 6421 2828516 (ROOM) Assistant Professor of Microbiology Department of Botany, Institute of Science Visva-Bharati (A Central University) Santiniketan, West Bengal 731235, India. E mail: bumba_mi...@visva-bhatari.ac.in, bumba_mi...@rediffmail.com; ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy
Re: [galaxy-user] Megablast question
Hi Scott I never used megablast so what i am writing is true of just any fasta file (so if there is anything quirky in megablast that i dont know about, apologies!): Take your fasta file and convert to tabular (under "fasta manipulation" - this will make it go to one line per record). Then randomly choose whatever number of reads you want using "select random lines from a file" under the text maniupulation tab. Then convert the tabular file back to fasta. (under the fasta manipulation tab) noa On 16/02/2012 19:31, Scott Tighe wrote: Hi all When using Galaxy megablast, is there a simple way to reduce my FASTA files from 23 million reads to 1/2 that size and submit to megablast separately? Thanks -- Scott Tighe Advanced Genome Technology Lab Vermont Cancer Center at the University of Vermont 149 Beaumont Avenue Health Science Research Bd RM 305 Burlington Vermont USA 05405 lab 802-656-AGTC (2482) cell 802-999- ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Error on custom builds on public galaxy server
I also had exactly the same problem yesterday - glad to see that maybe it wasn't just me. Happy for help! Noa On 16/02/2012 22:24, Pengfei Yu wrote: Dear sir or madam, I am using galaxy public server and I am trying to build a custom genome using the function "custom Builds" in "user" section. I specified the Name, Key and uploaded the genome fasta file also the chromosome length file. But when I click "submit", galaxy gave an error information like that: "" Server Error: An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) "" I don't know where to find the error logs and how to turn debug on. Could you tell me how to fix the problem and upload the custom builds? Thanks a lot! Pengfei -- Pengfei Yu Center of Biophysics and Computational Biology University of Illinois Urbana-Champaign Illinois, 61820, US Cell phone: 217-898-6301 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Running cufflinks on a genome without a bowtie index
Hi I am trying to run Cufflinks on a genome without a bowtie index. How do I make my own index? I have a FASTA file of the genome, but if I run tophat using just that and then cufflinks using a gtf file of the transcriptome, I get zero in all FPKM values Thanks Noa ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Problem creating GTF file for use with cufflinks
I am a non-programmer working on Prochlorococcus (a marine
bacteria) for which UCSC and Ensembl do not yet have
genome/transcriptome available or uploaded. However, the genome
and transcriptome of this organism have been solved and annotated
and are available on microbes online (http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=511145).
I have been trying to run transcriptome analyses using cufflinks,
for which I need gtf files of the transcriptome. Microbes online
has tab delimited files and I have been trying to convert them to
gtf files using excel. Basically, I reorganized the data so that
the first 8 columns seem fine when uploaded to galaxy. The way I
have been doing this is to save the file as a tab delimited excel
file, and then upload the file onto Galaxy by "telling" galaxy
that it is a gtf file (instead of allowing galaxy to identify the
file type itself using the auto-detect function) when using the
file upload option. However, when I do this, I cant get the 9th
column (attributes) to work.
I have tried either to separate the attributes in the 9th
column in my excel spreadsheet by either a space or a tab (using
concatenation with the char(9) function which I understand encodes
a tab in excel). In all cases, when I upload to galaxy by
identifying the .txt file as a .gtf file, the 9th column splits
into columns 9,10,11, etc when I use a char(9) function in excel)
or I get an error message from cufflinks (An error occurred
running this job: cufflinks v1.0.3 cufflinks -q
--no-update-check -I 30 -F 0.05 -j 0.05 -p 8 -G
/galaxy/main_database/files/003/377/dataset_3377315.dat Error
running cufflinks. [Errno 2] No such file or directory:
'transcripts.gtf') when I use spaces to separate the
attributes.
I would be happy to know whether there is a way to convert my tab
delimited transcriptome file from Microbes Online to a gtf file
(either by excel or another program) which would enable me to use
galaxy's NGS functions on Prochlorococcus.
Additionally, when I upload my data files I am able to choose the
prochlorococcus genome on galaxy (genome 213 in the 'upload file'
option), but am unable to chose it from the reference genome list
when performing tophat on galaxy. This may solve the problem (or
may be part of the same issue).
Many thanks,
Noa Sher
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[galaxy-user] there was a wrong link in my previous mail - gtf file issues
The correct link: http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919
Previous mail:
I am a non-programmer working on Prochlorococcus (a marine
bacteria) for which UCSC and Ensembl do not yet have
genome/transcriptome available or uploaded. However, the genome
and transcriptome of this organism have been solved and annotated
and are available on microbes online (http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919).
I have been trying to run transcriptome analyses using cufflinks,
for which I need gtf files of the transcriptome. Microbes online
has tab delimited files and I have been trying to convert them to
gtf files using excel. Basically, I reorganized the data so that
the first 8 columns seem fine when uploaded to galaxy. The way I
have been doing this is to save the file as a tab delimited excel
file, and then upload the file onto Galaxy by "telling" galaxy
that it is a gtf file (instead of allowing galaxy to identify the
file type itself using the auto-detect function) when using the
file upload option. However, when I do this, I cant get the 9th
column (attributes) to work.
I have tried either to separate the attributes in the 9th
column in my excel spreadsheet by either a space or a tab (using
concatenation with the char(9) function which I understand encodes
a tab in excel). In all cases, when I upload to galaxy by
identifying the .txt file as a .gtf file, the 9th column splits
into columns 9,10,11, etc when I use a char(9) function in excel)
or I get an error message from cufflinks (An error occurred
running this job: cufflinks v1.0.3 cufflinks -q
--no-update-check -I 30 -F 0.05 -j 0.05 -p 8 -G
/galaxy/main_database/files/003/377/dataset_3377315.dat Error
running cufflinks. [Errno 2] No such file or directory:
'transcripts.gtf') when I use spaces to separate the
attributes.
I would be happy to know whether there is a way to convert my tab
delimited transcriptome file from Microbes Online to a gtf file
(either by excel or another program) which would enable me to use
galaxy's NGS functions on Prochlorococcus.
Additionally, when I upload my data files I am able to choose the
prochlorococcus genome on galaxy (genome 213 in the 'upload file'
option), but am unable to chose it from the reference genome list
when performing tophat on galaxy. This may solve the problem (or
may be part of the same issue).
Many thanks,
Noa Sher
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues
Hi Hiram,
I managed to extract the columns in a different order (albeit I
did it in excel and not using command line) but then the 9th
column (attributes) of gtf is what I had problems with
Thanks
noa
On 04/12/2011 21:43, Hiram Clawson wrote:
Pardon me, I see there is only one that says "tab-delimited" file.
That is a tough one to decode. It almost looks like GTF already, but
not quite. If we take it as a simple file of annotations on the genome,
without structure such as exons, introns, and merely rework the columns
to turn it into a bed file. Extract columns in this order: 4,5,6,2,7
to get a bed file with the accession identities:
awk -F'\t' '{printf "%s\t%d\t%d\t%s\t%s\n", $4,$5,$6,$2,$7}' 59919.tab 59919.bed
It would take some time to figure out how to convert this file
to something useful since I am not familiar with the format.
I can't see immediately how to use it properly.
--Hiram
- Original Message -
From: "Noa Sher" noa.s...@gmail.com
To: "Hiram Clawson" hi...@soe.ucsc.edu
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:10:06 AM
Subject: Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues
Hi Hiram,
I was trying to work with the tab delineated file (using the link under export genomic data).
Thanks
noa
On 04/12/2011 20:29, Hiram Clawson wrote:
Good Morning Noa:
Which one of the files at microbesonline are you trying to work with ?
--Hiram
- Original Message -
From: "Noa Sher" noa.s...@gmail.com To: galaxy-user@lists.bx.psu.edu Sent: Sunday, December 4, 2011 1:38:35 AM
Subject: [galaxy-user] there was a wrong link in my previous mail - gtf file issues
The correct link: http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919
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Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
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use the Galaxy Development list:
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