Question: Bioscope With Cufflinks
0
gravatar for Ramon Vidal
7.9 years ago by
Ramon Vidal10
UdeM
Ramon Vidal10 wrote:

Does any one here have ever used Bioscope with Cufflinks to do DE analysis? I am trying to use the BAM files generated by Bioscope to do it but all my output files have zero expression values (fpkm 0.0). I am using the recommended parameter "--library-type fr-secondstrand" and I also tried to convert the BAM to SAM and add the XS:A[+-] flag but it didn't work also. I don't know if it is the cause but I have two of these errors: "SAM error on line nnnnnnn: CIGAR op has zero length". Thank you

cufflinks • 2.2k views
ADD COMMENTlink modified 4.5 years ago by Biostar ♦♦ 20 • written 7.9 years ago by Ramon Vidal10

There is also a thread here on SeqAnswers with similar issues: http://seqanswers.com/forums/showthread.php?t=3551

I always used TopHat with SOLiD RNA-seq data and it worked to get alignments ready for CuffLinks.

ADD REPLYlink written 7.9 years ago by Chris Penkett480
0
gravatar for r.follador
6.1 years ago by
r.follador60
Switzerland
r.follador60 wrote:

Doesn't directly answer your question, but I use following workflow to do DE analysis with SOLiD data:

I very much prefer DESeq over Cufflinks; see for example Bullard et al., 2010 why the RPKM approach is not adivsable.

ADD COMMENTlink written 6.1 years ago by r.follador60
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