Re: [galaxy-dev] Extracting bacterial seq from cordinates

[shamsher jagat]

Jen,

I have also shared history with you File 27 and 32 are fetching empty seq
file. I think since bacterial genome is not having any Chr that may be the
problem, I tried all option just coordinates; Chr1 however the out put is
empty.

Thanks

Kanwar

On Wed, Dec 19, 2012 at 10:07 AM, Jennifer Jackson  wrote:

>  Hello,
>
> Both datasets can be loaded and the "custom reference genome" option used
> with the tool 'Fetch Sequences -> Extract Genomic DNA". Details about
> custom genomes are grouped here in our:
> http://wiki.galaxyproject.org/Support#Custom_reference_genome
>
> To be specific, on the "Extract" tool form, you will use the option:
> "Source for Genomic Data:" as  "History", then for the new menu option
> "Using reference file:", select the fasta dataset of your genome from your
> active history.
>
> If you have trouble, be sure to double check that your formats match those
> required by the tool (listed on tool's form). Detailed custom genome
> troubleshooting help is in the wiki above and file format troubleshooting
> help is here, including links to data specifications:
> http://wiki.galaxyproject.org/Support#Troubleshooting_tool_errors
> (start here, more help in following sections, same wiki)
>
> Best,
>
> Jen
> Galaxy team
>
>
> On 12/19/12 8:19 AM, shamsher jagat wrote:
>
> I have a bacterial genome from ncbi and woulld like to extract seq from
> the corresponding fasta file of bacterial genome. Since i have list of
> coordinates so would not be possible to extract one by one. Is there any
> interface within galxy that i can use.
>
>  Thanks
>
>
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> --
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>
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[galaxy-dev] Extracting bacterial seq from cordinates

[shamsher jagat]

I have a bacterial genome from ncbi and woulld like to extract seq from the
corresponding fasta file of bacterial genome. Since i have list of
coordinates so would not be possible to extract one by one. Is there any
interface within galxy that i can use.

Thanks
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Re: [galaxy-dev] MACS not found

[shamsher jagat]

use CISTROME



On Tue, Dec 18, 2012 at 8:09 PM, Alfonso Garrido-Lecca <
alfonso.garrido-le...@colorado.edu> wrote:

> Hello,
> I am new in using galaxy on the cloud. I am trying to analyze my ChIP-seq
> data.
> However, when I try to run the MACS peak calling algorithm on my BAM files
> I get
> an error message saying "MACS: not found". Any ideas?
> thanks!
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Re: [galaxy-dev] The qiuck way to upload large file

[shamsher jagat]

FTP or URL

On Sat, Dec 1, 2012 at 5:37 AM, 泽 蔡  wrote:

> Hi all,
>
> I'm a new guy of galaxy and bioinformatics.
> I read the document of galaxy, but it's so hard to find what I need.
> I already set up a locale instance of galaxy, it works fine. The problem
> is I need to analysis large data, but the "upload file" is so slow, is
> there some ways I can upload large file quickly?
>
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Re: [galaxy-dev] how to get annotation files for rna-seq

[shamsher jagat]

Can we also fetch virus file from some sources like this?

Thanks

Kanwar

On Mon, Nov 26, 2012 at 4:25 AM, Joachim Jacob  wrote:

> You can use 'Get data' --> 'UCSC Main' to fetch an GTF (gene transfer
> format) format of your species of interest, Human in this case. I tend to
> use the Ensembl genes track (from the Genes and gene prediction tracks).
>
> Make sure you use GTF as output, and send to Galaxy!
>
> Cheers,
> Joachim
>
> Joachim Jacob, PhD
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
> On 11/26/2012 01:07 PM, Dr. Mira A. Bisso wrote:
>
>>
>> Dear help;
>>
>> How to get the human annotation file for RNAseq analysis, for mapping by
>> BWA and for RNAseq analysis, on Cufflinks and cuffdiff tools on galaxy?
>>
>> Mira
>>
>> Thanks
>>
>> *image001*
>>
>> **
>>
>> *Mira Bosso, M.Sc, B.D.S*
>>
>> *Research associate*
>>
>> *Pancreatic Islet Biology and Transplantation Unit*
>>
>> *P.O.Box 1180, Dasman 15462, Kuwait
>> Phone:  +965 2224 2999 Ext.2803*
>>
>> *Mob: +96599500197 *
>>
>> *Email: mira.bi...@dasmaninstitute.org > dasmaninstitute.org >*
>>
>> **
>>
>>
>>
>> __**_
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>
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[galaxy-dev] Question about SNP calling

[shamsher jagat]

Is there a work flow/ tutorial how to call SNP and get significant SNP
followed by their annotation.

Thanks
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Re: [galaxy-dev] Incomplete datasets when dowloaded from history

[shamsher jagat]

I was never able to donwload data from history (Penn state server). I would
be intersted to see the feedback on this quetion.

Thanks.

On Wed, Jun 6, 2012 at 6:53 AM, Jean-Francois Payotte <
jean-francois.payo...@dnalandmarks.ca> wrote:

> Hi folks,
>
> Some of our local Galaxy instance users seem to be experiencing some
> strange behaviour lately.  I searched the mailing-list archive but I didn't
> found anything related, so I'd be interested to know if somebody already
> had the same issue.
>
> The problem is that sometimes, when people are trying to download their
> datasets from their history, although the file seems to download
> successfully, it appears that the downloaded file is incomplete (for
> example a 3000 lines text file will show only maybe 2000 lines at the first
> download, 1600 lines at the second download, and so on... and eventually,
> the file will download completely.
>
> This issue happened with more than one user and with different tools.
>
> Does anybody ever had this kind of issue?  Or does somebody would have an
> idea of where to look to solve this problem?
>
> Best regards,
> Jean-François
>
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[galaxy-dev] TSS for list of genes

[shamsher jagat]

I am not sure if this is the right place to post this message, I want to
download TSS fro a list of around 1000 human genes. Is this something I can
do in Galaxy?
Thanks.
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Re: [galaxy-dev] Fwd: Your message to galaxy-dev awaits moderator approval

[shamsher jagat]

I have also been getting such messages and even saying there are too
many re-bounces so your account is being disabled and I can not reactivate
using the link sent in email

On Sun, May 22, 2011 at 11:28 PM, shashi shekhar wrote:

>
>
> -- Forwarded message --
> From: 
> Date: Mon, May 23, 2011 at 11:42 AM
> Subject: Your message to galaxy-dev awaits moderator approval
> To: meshash...@gmail.com
>
>
> Your mail to 'galaxy-dev' with the subject
>
>requirement of complete command in code file
>
> Is being held until the list moderator can review it for approval.
>
> The reason it is being held:
>
>Post by non-member to a members-only list
>
> Either the message will get posted to the list, or you will receive
> notification of the moderator's decision.  If you would like to cancel
> this posting, please visit the following URL:
>
>
> http://lists.bx.psu.edu/confirm/galaxy-dev/32ca9fa0742b2f4b3a3e5ad2f9c57f06783f8188
>
>
>
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Re: [galaxy-dev] question about Filtering Cufflink files

[shamsher jagat]

Further to my question, It appear that there is some problem with the filter
option:

When I use the isoform/gene exp file as such it work fine but when I filter
these files with either parameter such as status if test was successful or
on p value it return me empty file. The way am saving the file is - expr
file filter save as txt file and upload back in Galaxy.

Any suggestion?



Jagat

On Tue, May 3, 2011 at 3:08 AM, shamsher jagat  wrote:

> Jeremy,
>
> I have been trying to follow  the steps in filtering Cufflink out put files
> you have  described in one of the previous messages (
> http://gmod.827538.n3.nabble.com/Re-downstream-analysis-of-cuffdiff-out-put-td2836457.html
> ):
>
> I have shared histroy with you, but in summary:
>
>
> File 35: when Filter GTF data by attributes value list on data 11 (combined
> GTF) and data 33 (which is gene expr  file) . Will not this should have
> one gene per row. But it is not?
>
> File 39:  Filter GTF file by attribute value list on data 11 and data 38
> (Cuffdiff splicing expr) it failed. I would assume that it should filter  on
> the basis of TSSid . The error message is
>
> Traceback (most recent call last):
>
>   File
> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
> line 67, in
>
> filter( gff_file, attribute_name, ids_file, output_file )
>
>   File
> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
> line 57, in filter
>
> if attributes[ attribute_name ] in ids_dict:
>
> KeyError: 'tss_id'
>
> 40 : Filter GTF data by attribute list on data 11 and 34 (tss group exp)
> failed and error message is:
>
> Traceback (most recent call last):
>
>   File 
> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
>  line 67, in
>
> filter( gff_file, attribute_name, ids_file, output_file )
>
>   File 
> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
>  line 57, in filter
>
> if attributes[ attribute_name ] in ids_dict:
>
> KeyError: 'tss_id'
>
>
>
> I would consider that if one gene has different Id than there is splicing .
>
> However in contrast isoform file with transcript Id is working fine (File
> 20)
>
>  On a different note can I convert GTF file to txt tab delaminated file I
> tried to convert file 11 in txt (following Edit attributes) but the file is
> not properly formatted especially col-pid and TSS id. Am I doing something
> wrong.
>
> Thanks.
>
>
>
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[galaxy-dev] question about Filtering Cufflink files

[shamsher jagat]

Jeremy,

I have been trying to follow  the steps in filtering Cufflink out put files
you have  described in one of the previous messages (
http://gmod.827538.n3.nabble.com/Re-downstream-analysis-of-cuffdiff-out-put-td2836457.html
):

I have shared histroy with you, but in summary:


File 35: when Filter GTF data by attributes value list on data 11 (combined
GTF) and data 33 (which is gene expr  file) . Will not this should have one
gene per row. But it is not?

File 39:  Filter GTF file by attribute value list on data 11 and data 38
(Cuffdiff splicing expr) it failed. I would assume that it should filter  on
the basis of TSSid . The error message is

Traceback (most recent call last):

  File
"/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
line 67, in

filter( gff_file, attribute_name, ids_file, output_file )

  File
"/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
line 57, in filter

if attributes[ attribute_name ] in ids_dict:

KeyError: 'tss_id'

40 : Filter GTF data by attribute list on data 11 and 34 (tss group exp)
failed and error message is:

Traceback (most recent call last):

  File 
"/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
line 67, in

filter( gff_file, attribute_name, ids_file, output_file )

  File 
"/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
line 57, in filter

if attributes[ attribute_name ] in ids_dict:

KeyError: 'tss_id'



I would consider that if one gene has different Id than there is splicing .

However in contrast isoform file with transcript Id is working fine (File
20)

 On a different note can I convert GTF file to txt tab delaminated file I
tried to convert file 11 in txt (following Edit attributes) but the file is
not properly formatted especially col-pid and TSS id. Am I doing something
wrong.

Thanks.
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[galaxy-dev] getting genome coordinates

[shamsher jagat]

Is it possible to extract genomic coordinates If I have gene accession ID
Chr stat and end position. Any pointer will be helpful.

Thanks.
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