Bioscope With Cufflinks
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12.6 years ago
Ramon Vidal ▴ 10

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 • 3.1k views
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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.

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10.8 years ago
r.follador ▴ 90

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.

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