[galaxy-user] Upload files to Galaxy via FTP

2013-06-11 Thread Hoang, Thanh
Hi, I have been trying to upload my RNA-seq data files (~20 Gb total) via FTP using my account in Galaxy. But I could not connect to the server. The following message showed up: *Error: Critical error* *Error: Could not connect to server* Could you suggest any idea to overcome this problem? Thank

Re: [galaxy-user] FTP upload problem

2013-06-11 Thread Hoang, Thanh
Hi all, I just finished uploading 2 files via FTP and I have some more files to be uploaded. After an Internet disconnection, I got the same problem like Delong had. I got this message: 530 Sorry, the maximum number of clients (3) for this user are already connected Error: Critical error Error:

Re: [galaxy-user] FTP upload problem

2013-06-12 Thread Hoang, Thanh
, Hoang, Thanh wrote: Hi all, I just finished uploading 2 files via FTP and I have some more files to be uploaded. After an Internet disconnection, I got the same problem like Delong had. I got this message: 530 Sorry, the maximum number of clients (3) for this user are already connected Error

[galaxy-user] Get Gene name from Cuffdiff's output?

2013-06-17 Thread Hoang, Thanh
Hi guys, I am trying to examine gene differential expression in my mouse samples using : Cufflink CuffmergeCuffdiff The output from Cuffdiff shows only gene id, but not gene name: test_id gene_idgenelocussample_1 sample_2 XLOC_01XLOC_01-

[galaxy-user] How to define the cutoff value of RPKM for expressed genes?

2013-07-03 Thread Hoang, Thanh
Hi all, I have been working on RNA-seq data analysis using TopHat and Cuffdiff. One of the problem I have is to define the cutoff RPKM value to tell whether a gene is expressed from the background noise?. Could anybody give me a suggestion? Thank you Thanh

[galaxy-user] Evaluating TopHat's results

2013-07-14 Thread Hoang, Thanh
Hi, I ran TopHat on Galaxy for my RNA-seq data. I want to analyze TopHat's output files, such as percentage of reads mapped to the genome...but I am not sure how to do that. I am also trying to visualize the BAM file by IGB but the following error message appears : Failed to authenticate to the

Re: [galaxy-user] Evaluating TopHat's results

2013-07-15 Thread Hoang, Thanh
, let us know about the second, Take care, Jen Galaxy team On 7/14/13 1:47 PM, Hoang, Thanh wrote: Hi, I ran TopHat on Galaxy for my RNA-seq data. I want to analyze TopHat's output files, such as percentage of reads mapped to the genome...but I am not sure how to do that. I am also

[galaxy-user] Problem with repeated genes in Cuffdiff's output

2013-07-16 Thread Hoang, Thanh
Hi all, I am working on RNA-seq using TopHat/Cufflink/Cuffdiff for differential gene expression and new gene discovery ( this is what I am interested in). However, I found many genes that are repeated in the Cuffdiff's ouput. These are the same genes and at the exact the same locus. There should

[galaxy-user] Exceptionally high RPKM values of miRNA and other short genes in Cuffdiff's output

2013-07-18 Thread Hoang, Thanh
Hi all, I have been analyzing my RNA-seq data on mouse tissues. My RNA-data is single-ended and 51 bp in length. I ran TopHat/Cufflink/Cuffdiff to test to differential gene expression In the Cuffdiff's output, I got very high RPKM value for some of miRNA and some other short genes ( less than

Re: [galaxy-user] Exceptionally high RPKM values of miRNA and other short genes in Cuffdiff's output

2013-07-19 Thread Hoang, Thanh
in the next week or two as we sort out a sane and generalised Atlas dependency installation. On Fri, Jul 19, 2013 at 2:55 AM, Hoang, Thanh hoan...@miamioh.edu wrote: Hi all, I have been analyzing my RNA-seq data on mouse tissues. My RNA-data is single-ended and 51 bp in length. I ran TopHat

[galaxy-user] Significant in Cuffdiff's ouput

2013-07-19 Thread Hoang, Thanh
Hi all, I have some questions about how Cufffdiff does the statistical analysis. I am looking for DE genes in two sample groups ( 3 replicate per group). In the Cuffdiff;s gene_exp.diff, I found many genes that have very large RPKM fold-change between two groups (with p value or 0.05) but

[galaxy-user] miRNA analysis

2013-09-18 Thread Hoang, Thanh
Hi all, I would like to analyze my miRNA sequencing analysis from mouse tissue. I have not any idea which tools or pipeline work best. Do you have any suggestion? Regards Thanh ___ The Galaxy User list should be used for the discussion of

Re: [galaxy-user] miRNA analysis

2013-09-18 Thread Hoang, Thanh
documentation, that you can review to see if the tool is a good fit for what you want to do (if it is not expression analysis anymore, or you want to try something different like DESeq). http://toolshed.g2.bx.psu.edu/repository Hopefully this helps, Jen Galaxy team On 9/18/13 10:19 AM, Hoang, Thanh

[galaxy-user] 3' adapter trimming using FASTX-toolkit clipper

2013-09-19 Thread Hoang, Thanh
Hi all, I am analyzing miRNA sequencing now. My data is 51bp, single -ended and ~5 M reads. I want to remove the adapter sequences from the reads before mapping to the genomes/known miRNA database. My 3' adapter sequence is : 5-AGATCGGAAGAGCACACGTCT-3. I found that many reads only contain part of

[galaxy-user] RNA-DNA converter in Fasta format

2013-09-21 Thread Hoang, Thanh
Hi all, I want to to map my sequencing reads to miRNA reference database . Anyone know how to convert RNA to DNA in FASTA format ( U to T) . Thanks Thanh ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other

Re: [galaxy-user] RNA-DNA converter in Fasta format

2013-09-22 Thread Hoang, Thanh
Thank you Bjoern, I figured it out. Just use Fastx nucleotide exchanger.in Fastx-toolkit Thanh On Sun, Sep 22, 2013 at 4:51 AM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Thanh, under FASTA manipulation I have one tool das is called RNA/DNA converter. If it is not

[galaxy-user] non-coding RNA annotation

2013-09-22 Thread Hoang, Thanh
Hi all, I am analyzing my small RNA sequencing data on mouse tissue. Does anyone know where to download annotation file for non-coding RNA? Thanks Thanh ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other

[galaxy-user] Can TopHat take SNPs into account?

2013-10-02 Thread Hoang, Thanh
Hi, I have been mapping my RNA-seq data to mouse genome from a different mouse strain using TopHat. I am wondering whether TopHat can take SNPs into account during the alignment? ( using SNPs track as an optional input)? Thanks Thanh ___ The

Re: [galaxy-user] miRNA-seq help

2013-10-11 Thread Hoang, Thanh
Hi Calvin, I am analyzing miRNA differential expression from my small RNA sequencing data from mouse tissue using Bowtie HtseqDeseq. I tried both whole mouse genome and hairpin miRNA( from miRbase) as reference sequences and annotation of all known miRNA (from miRbase). These worked for me.