Re: [galaxy-user] cuffmerge
Hello Janice, Are you using the public Main Galaxy instance at http://usegalaxy.org? Would you be able to submit this as a bug report? Thanks, Jen Galaxy team On 2/10/14 11:07 AM, Janice Patterson wrote: I am analyzing RNA-seq data and I ran Cufflinks with the genes.gtf as a reference annotation guide, with bias correction using the genome.fa as a reference. When I subsequently attempt to run cuffmerge on my assembled transcript files, however, I get the following errors, and cuffmerge fails. Error: duplicate GFF ID 'CUFF.1.1' encountered! [FAILED] Error: could not execute gtf_to_sam I am using the same genes.gtf file I used for cufflinks. It is the genes.gtf file attained from the Data Libraries provided by galaxy. I ran Cufflinks on the same data set without bias correction (and therefore a genome.fa file was unnecessary) and no multi-read correct, and subsequent cuffmerge with the same genes.gtf file provided ran just fine. Why did turning on bias correction and providing cufflinks with a fasta reference file making cuffmerge fail? Thanks. Janice Patterson ___ 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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] cuffmerge loses p_id
Hello Christopher, We did some testing here using your available data and are fairly certain that the problem is with the tool itself and not the Galaxy wrapper. Contacting the author and asking about the issue is probably the best way forward. If you have time, we would be glad to learn about the outcome. Best, Jen Galaxy team On 5/15/12 1:38 PM, Christopher M. Weber wrote: Hello, Problem: Cuffmerge loses p_id from reference genome in merged gtf file on Galaxy online server resulting in blank cds cuffdiff files. DATA Input to Cuffmerge or Cuffcompare: Two fly cufflinks transcript assemblies created from bam files in Galaxy server using reference annotation and bias correction. Options: Use Reference Annotation: YES UCSC DM3 genes gtf (D. melanogaster) or ENSMBL 5.25 genes gtf Use Sequence Data: YES Result: tss_id found in cuffmerge but no p_id with either reference annotation file. Examples included below. Reference: 2L protein_coding stop_codon 86088610. + 0 exon_number 2; gene_id FBgn0031208; gene_name CG11023; p_id P13746; transcript_id FBtr0300689; transcript_name CG11023-RB; tss_id TSS8369; Cuffmerge: Cufflinks exon81939484. + . gene_id XLOC_01; transcript_id TCONS_0001; exon_number 2; gene_name CG11023; oId FBtr0300689; nearest_ref FBtr0300689; class_code =; tss_id TSS1; 2L Cufflinks exon66721 67003 . + . gene_id XLOC_02; transcript_id TCONS_0003; exon_number 1; gene_name dbr; oId CUFF.1.1; nearest_ref FBtr0078100; class_code j; tss_id TSS2; Help is much appreciated, Thanks! ___ 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://galaxyproject.org ___ 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] cuffmerge loses p_id
Hello Christopher, I see that this was also posted at SeqAnswers yesterday. I searched and didn't see anything specifically in the manual or at seqanswers that addresses this (but if someone else can find it, please add to this thread): http://seqanswers.com/forums/showthread.php?t=20084 Do you think this is a problem with the Cuffmerge program itself? If so, going to the authors is the next step by emailing tophat.cuffli...@gmail.com http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results (See: /Example/: *unexpected results with* /*RNA-seq analysis*/ *tools.)* * *If you think this is a problem may be with the Galaxy wrapper around CuffMerge, we can take a closer look. Please share a link to your history containing this data. Use Options (top 'gear' icon in history panel) - Share or publish, generate a share link, copy link, and email link back directly to me. Note the dataset #'s involved and leave all datasets unhidden/undeleted. Thanks! Jen Galaxy team On 5/15/12 1:38 PM, Christopher M. Weber wrote: Hello, Problem: Cuffmerge loses p_id from reference genome in merged gtf file on Galaxy online server resulting in blank cds cuffdiff files. DATA Input to Cuffmerge or Cuffcompare: Two fly cufflinks transcript assemblies created from bam files in Galaxy server using reference annotation and bias correction. Options: Use Reference Annotation: YES UCSC DM3 genes gtf (D. melanogaster) or ENSMBL 5.25 genes gtf Use Sequence Data: YES Result: tss_id found in cuffmerge but no p_id with either reference annotation file. Examples included below. Reference: 2L protein_coding stop_codon 8608 8610 . + 0 exon_number 2; gene_id FBgn0031208; gene_name CG11023; p_id P13746; transcript_id FBtr0300689; transcript_name CG11023-RB; tss_id TSS8369; Cuffmerge: Cufflinks exon 8193 9484 . + . gene_id XLOC_01; transcript_id TCONS_0001; exon_number 2; gene_name CG11023; oId FBtr0300689; nearest_ref FBtr0300689; class_code =; tss_id TSS1; 2L Cufflinks exon 66721 67003 . + . gene_id XLOC_02; transcript_id TCONS_0003; exon_number 1; gene_name dbr; oId CUFF.1.1; nearest_ref FBtr0078100; class_code j; tss_id TSS2; Help is much appreciated, Thanks! ___ 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://galaxyproject.org ___ 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] cuffmerge question
Carol, My question is, if I use the public Galaxy server interface to TopHat and Cufflinks, is there any access to cuffmerge? No, Cuffmerge is not available in Galaxy. Also, I'm trying to understand the difference between using cuffmerge and then using cuffcompare (without a reference genome) to assemble gtf transcript files produced by Cufflinks for each group of 3 Illumina paired-end reads corresponding to biological replicates, in order to use the resulting combined gtf file for comparing the TopHat alignments of two such groups using cuffdiff. Is there any difference in the output between cuffdiff and cuffcompare, using in this fashion? For example, do they form the union of transcripts by the same rules, and do their outputs contain (or lack) the same columns (strand, perhaps??) I've read things on seq-answers indicating that I should be using cuffmerge, but I can't find it on the public server and apparently haven't installed it properly on my own computer so far. From the Cufflinks/compare/merge/diff documentation ( http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge ): *Cuffmerge calls Cuffcompare and does some filtering of transfrags as well as merging of novel and known isoforms; *The main purpose of this script is to make it easier to make an assembly GTF file suitable for use with Cuffdiff. Hence, it appears that Cuffmerge and Cuffcompare are relatively similar and use the same basic union algorithm--whatever Cuffcompare uses. If you have more detailed questioned, you might ask the Cufflinks' authors: tophat.cuffli...@gmail.com Good luck, J.___ 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/
