[galaxy-user] RNA-Seq analysis
Since the pictures are too big for the mailling list. I will upload it in seperate emails. Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed transcripts and differentially expressed genes. In these two lists, I would like to see the gene name, gene ID and transcript ID. What I did is: I run cufflinks using reference gene sets (GTF file) from Ensembl (see picture human Chr19 refgene). I modified the ensembl GTF file according to http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq4 so that cufflinks can recognize the column for chromosomes. I got cufflinks assembled transcript which shows nicely the gene ID, transcript ID (see picture Cufflinks assembled transcript), but the gene name was lost in this file. Then I run cuffcompare using the same reference gene sets (GTF file) from Ensembl. In the output file (picture cuffcompare combined transcript) you can see that gene name appeared, but galaxy assigned new ID to gene and transcript. Then I run cuffdiff . Output file (see picture Cuffdiff transcript differential expression) only contains gene name. My question is: how can I keep the information from the reference gene sets during the whole analysis process so that I get meaningful information. Or it is that possible that I retrieve gene ID, transcripte ID by using the output file Cuffdiff transcript differential expression from cuffdiff? I hope you can help me. Many thanks in advance. JIwen___ 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] Question about uploading custom index for bowtie
I recently tried to upload a custom made index for bowtie using Filezilla as my FTP source, but I got an error message, I think due to the autodetect for file type not recognizing this file type. Is there something special that I should do to upload my six .ebwt files for my reference? ___ 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] Question about uploading custom index for bowtie
Hello William, To use a custom reference genome, all you need to upload is the single fasta file for the genome. Galaxy will do the rest and create indexes as appropriate. Hopefully this helps! Thanks, Jen Galaxy team On 2/6/12 11:51 AM, William Light wrote: I recently tried to upload a custom made index for bowtie using Filezilla as my FTP source, but I got an error message, I think due to the autodetect for file type not recognizing this file type. Is there something special that I should do to upload my six .ebwt files for my reference? ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
