[galaxy-user] merging fastq files

Hi I have received Illumina paired-end genome sequence data as a .tar file. When unpacked the data for each genome accession is split into about 100 fastq files. Total of about 37 Gpb per genome. Can you recommend the best way to organise this data prior to mapping to reference genome? I can con

[galaxy-user] (no subject)

Dear Galaxy team, I have a question about RNA analysis with the cufflinks package. I have some bam files to analyze from a SOLiD platform. Some previous tests show that these bam/sam files are different from those coming from Tophat and cufflinks cannot assemble them using a reference annotatio

Re: [galaxy-user] FastQC Issue with per base nucleotide quality graph

Justin: Can you share a history with me via a link (click gear on the top rigt, choose "share or publish" and click "Make history accessible via a link"; then e-mail this link to me). I'll see what is happening. Tx, a. Anton Nekrutenko http://www.galaxyproject.org On Mar 28, 2013, at 10:41

[galaxy-user] Parameters for merging BAM files

Hi All, I want to merge the Tophat output (Accepted Hits) of Several datasets. I want the merged BAM file has the exact format as the individual input BAM files, should I check "Merge all component bam file headers into the merged bam file"? Thanks. Have a nice weekend. Jianguang

Re: [galaxy-user] (no subject)

Cuffmerge does some additional steps that Cuffcompare does not; specifically, Cuffmerge attempts to remove assembly artifacts: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge It's likely that the (presumed) artifacts removed by Cuffmerge account for the differences that you're seeing. Best

[galaxy-user] tophat job help

Hi, I have been running a tophat job and it seems to run forever, its now 24 HRS . I do not understand, is it that i have done something wrong, the other tophat job took only 6 hrs. please help regards, Dipanjana -- *Dipanjana Datta De* *Postdoctoral Fellow* *Department of Pharmacology and Toxico