Re: [galaxy-user] miRNA NGS data processing

2011-08-09 Thread yao chen
Hi Mete, I am not sure it is the sort problem. I find cufflinks in galaxy is unstable. I have bam files from Tophat which I can run cufflinks a few days agao. But these days when I run cufflinks with these bam files, the error shows. Strangely, it can work some time. I don't know the reason.

Re: [galaxy-user] miRNA NGS data processing

2011-08-09 Thread David Matthews
Hi, Tophat may still be an option for you. You can filter out spliced reads by filtering column 6 (the CIGAR column) for reads that only map directly (i.e. c6=='56M' if you have a 56bp paired end read). But I agree with Jen that most likely it is a sort problem. Best Wishes, David.

Re: [galaxy-user] miRNA NGS data processing

2011-08-08 Thread Jennifer Jackson
Hi Mete, This FAQ has a workflow for sorting a Bowtie (or any) SAM file for Cufflinks: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2 Thanks! Jen Galaxy team On 8/4/11 10:27 AM, Mete Civelek wrote: Hi, I'm trying to get read counts or FPKM values for my miRNA NGS

[galaxy-user] miRNA NGS data processing

2011-08-04 Thread Mete Civelek
Hi, I'm trying to get read counts or FPKM values for my miRNA NGS data on Galaxy. I have aligned the reads using Bowtie, but it appears that Cufflinks gives an error when run on the Bowtie alignments (This might have something to do with Bowtie's BAM file not being sorted). I know that Tophat