Question: Rnaseq Analysis Questions
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gravatar for Aarti Desai
7.0 years ago by
Aarti Desai20
Aarti Desai20 wrote:
Hi, I am using galaxy to analyze some RNASeq data. I have a couple of questions with regards to it: 1. When we are uploading data, one of the fields to be populated is "Genome". Why or where is galaxy using the genome information during file upload? 2. During Cuffcompare analysis, we can provide 3 files, two GTF files output from cufflinks and a reference annotation file. When cuffcompare how does it use the annotation file? 3. If cuffcompare is run using one cufflink GTF file and one reference annotation file, what are we supposed to do during cuffdiff analysis where you have to provide 2 sam/bam files? Is there any documentation/manual (except for what is on the UI) around that can help answers these (and some other basic questions I have). Thanks a lot for your help. Regards, Aarti
rna-seq cufflinks • 1.0k views
ADD COMMENTlink modified 7.0 years ago by Jeremy Goecks2.2k • written 7.0 years ago by Aarti Desai20
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gravatar for Jeremy Goecks
7.0 years ago by
Jeremy Goecks2.2k
Jeremy Goecks2.2k wrote:
Hello Aarti, Genome data is not used during upload but is often used subsequently. Because it's often an important piece of metadata, Galaxy encourages users to set it immediately on upload. This question is best addressed by reading the Cuffcompare documentation: http://cufflinks.cbcb.umd.edu/manual.html#cuffcompare Cuffdiff is only appropriate for comparing RNA-seq samples. More information can be found in the cuffdiff docuementation: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff Yes, the original Cufflinks paper: http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html and the Cufflinks manual: http://cufflinks.cbcb.umd.edu/manual.html will help you understand how to use Cufflinks/compare/diff. Thanks, J.
ADD COMMENTlink written 7.0 years ago by Jeremy Goecks2.2k
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