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Forum: Bioinformatics 11-30-2011, 12:24 PM
Replies: 2
Views: 2,120
Posted By cw11
Maybe try aligning with Tophat? CuffDiff is...

Maybe try aligning with Tophat? CuffDiff is designed to take Tophat output.
Forum: Bioinformatics 11-30-2011, 12:23 PM
Replies: 3
Views: 3,297
Posted By cw11
Side note - which version are you using? (I ask...

Side note - which version are you using? (I ask because there were some problems with 1.1.0 listing FPKMs as 0 when there were actually reads that mapped to those genes). I think they fixed this...
Forum: Bioinformatics 11-30-2011, 06:05 AM
Replies: 3
Views: 1,862
Posted By cw11
Effect of outlier sample on CuffDiff analysis?

Unless I'm much mistaken, CuffDiff pools reads from all samples within a condition prior to differential expression analysis. Does anyone understand the method by which CuffDiff prevents an outlier...
Forum: Bioinformatics 11-23-2011, 12:12 PM
Replies: 2
Views: 2,368
Posted By cw11
Responding to your last point first, I think the...

Responding to your last point first, I think the repeated genes in gene_short_name occur because some genes have multiple transcription start IDs. I notice that each of the repeat short names has a...
Forum: Bioinformatics 11-20-2011, 06:56 AM
Replies: 8
Views: 43,010
Posted By cw11
This site...

This site (http://www.eurofinsdna.com/service-corner/faqs-products-services/faqs-genome-sequencing/questions-on-genome-sequencing-services/what-is-a-mate-pair-library.html) describes some of the...
Forum: Bioinformatics 11-15-2011, 11:50 AM
Replies: 3
Views: 4,056
Posted By cw11
Hmm, I just saw a reply from Cole...

Hmm, I just saw a reply from Cole (http://seqanswers.com/forums/showpost.php?p=56767&postcount=9) on another thread (http://seqanswers.com/forums/showthread.php?t=14864) that might be relevant:
Forum: Bioinformatics 11-15-2011, 11:46 AM
Replies: 3
Views: 3,016
Posted By cw11
Regarding your first question: In Cufflinks, the...

Regarding your first question: In Cufflinks, the -g option gives you reference annotation based assembly (described here...
Forum: Bioinformatics 11-15-2011, 08:11 AM
Replies: 6
Views: 23,006
Posted By cw11
Yup - Glad you found an answer!

Yup - Glad you found an answer!
Forum: Bioinformatics 11-15-2011, 06:42 AM
Replies: 6
Views: 23,006
Posted By cw11
I'm not sure about Picard specifically, but I...

I'm not sure about Picard specifically, but I found a thread that discusses insert size here (http://seqanswers.com/forums/showthread.php?t=13098), which seems to suggest that the insert size is the...
Forum: Bioinformatics 11-15-2011, 05:54 AM
Replies: 4
Views: 4,133
Posted By cw11
Thanks! What has everyone doing to deal with...

Thanks! What has everyone doing to deal with these false positives? Just filtering out genes which have FPKMs of 0 for one of the conditions?

(I also understand from a different thread -...
Forum: Bioinformatics 11-15-2011, 05:35 AM
Replies: 17
Views: 7,455
Posted By cw11
Glad to hear that a fix is on the way! Will the...

Glad to hear that a fix is on the way! Will the fix address the problem of false positives as well? I'm using CuffDiff 1.1.0 and I've noticed that a lot of the genes I'm getting as differentially...
Forum: Bioinformatics 11-14-2011, 07:25 AM
Replies: 4
Views: 4,133
Posted By cw11
Question CuffDiff 0 FPKM Output/Incorrectly Identified Differential Expression?

Im having some problems with CuffDiff or rather, the output I am getting is completely baffling to me. I believe the program is incorrectly identifying genes as differentially expressed due to an...
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