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Can I Use *.Bam Generated By Tophat As Input For Coveragebed For Read Count Of Rna-Seq

It should be mapped by TopHat as it is indicated in the file name.

  1. Can I use this TopHat bam file as input of CoverageBed to count the read?
  2. If yes, which GTF/GFF file I should use ?

On the other hand,

I run cufflinks ,cuffmerg and cuffdiff. But the result is no gene is significantly differentially expressed. Where did I do wrong ? How to improve?

THANK YOU VERY MUCH!

rna-seq tophat
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written by whuanfan • whuanfan

Regardless of what genome those BAM files were aligned to, don't use coverageBed to get per-gene counts. If a read aligns to more than one feature, it increments the counter for both, which is the wrong way to do things when dealing with RNAseq. Use featureCounts (from subRead) or htseq-counts instead.

• 140 views • link
written by Devon Ryan Devon Ryan

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