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Forum: Bioinformatics

11-30-2011, 12:24 PM

Replies: 2

cufflinks error

Views: 2,546

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

Interpreting an FPKM of 0

Views: 3,796

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

Effect of outlier sample on CuffDiff analysis?

Views: 2,252

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

Downstream Cuffdiff analysis

Views: 2,903

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

paired-end vs. mate-pair

Views: 46,029

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

Inconsistency between cuffdiff 1.1.0 and cuffdiff 1.0.2

Views: 4,681

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

cuffmerge output

Views: 3,453

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

Insert size != Fragment size?

Views: 24,652

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

Insert size != Fragment size?

Views: 24,652

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

CuffDiff 0 FPKM Output/Incorrectly Identified Differential Expression?

Views: 4,873

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

Cufflinks "FAIL" Expression Estimates

Views: 8,822

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

CuffDiff 0 FPKM Output/Incorrectly Identified Differential Expression?

Views: 4,873

Posted By cw11

CuffDiff 0 FPKM Output/Incorrectly Identified Differential Expression?

I’m 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...

Showing results 1 to 12 of 12

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