Question: Can I Use *.Bam Generated By Tophat As Input For Coveragebed For Read Count Of Rna-Seq
0
gravatar for whuanfan
5.7 years ago by
whuanfan0
whuanfan0 wrote:

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!

tophat rna-seq • 1.9k views
ADD COMMENTlink written 5.7 years ago by whuanfan0
2

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.

ADD REPLYlink written 5.7 years ago by Devon Ryan91k

THANK YOU VERY MUCH !

ADD REPLYlink written 5.7 years ago by whuanfan0
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