Cufflinks and Comparison Analysis

DrD2009 · 03-10-2010, 01:40 PM

Hello everyone,

My goal is to start with 8 solexa sequenced mutants and compare their expressions.

So far I've performed the following steps to lead to Cufflinks analysis:
1.) Removed adapters from sequences.
2.) Mapped sequences using Bowtie with an output of SAM format.
3.) Sorted the SAM files.

Here is where my problem seems to come in. I have a bunch of files in GFF format that I want to compare my mutants to in order to say, X read is a miRNA, Y read is a siRNA, etc instead of having just chromosome coordinates. The end result is I want to say that X miRNA is present in mutant 1, 2, 3, ...n and their expressions are xxx.xx. I've tried this, but there has been no assignment to the reads with what they are or could be part of.

Can anyone offer some advise on my situation?

Thanks,
Brandon

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03-10-2010, 01:40 PM	#1
DrD2009 Member Location: Kansas City Join Date: Oct 2009 Posts: 88	Cufflinks and Comparison Analysis Hello everyone, My goal is to start with 8 solexa sequenced mutants and compare their expressions. So far I've performed the following steps to lead to Cufflinks analysis: 1.) Removed adapters from sequences. 2.) Mapped sequences using Bowtie with an output of SAM format. 3.) Sorted the SAM files. Here is where my problem seems to come in. I have a bunch of files in GFF format that I want to compare my mutants to in order to say, X read is a miRNA, Y read is a siRNA, etc instead of having just chromosome coordinates. The end result is I want to say that X miRNA is present in mutant 1, 2, 3, ...n and their expressions are xxx.xx. I've tried this, but there has been no assignment to the reads with what they are or could be part of. Can anyone offer some advise on my situation? Thanks, Brandon