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 AM,

[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.