Question: when using htseq-count, should I only count read-pairs whose two mates were both reported ?
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gravatar for lin.pei26
3.5 years ago by
lin.pei2670
China
lin.pei2670 wrote:

Hi all:

Working with pair-end RNA-seq data,

I found that for some read-pairs, only one end/mate was reported by tophat-output sam file and then htseq-count.

For such cases, what would you do in usual when calculating gene-wise read count ?

( I think I should only count those read-pairs whose both ends were successfully aligned and reported by htseq-count. )

Your opinions must be very valuable.

Thanks in advance!

Best,

 

rna-seq • 1.3k views
ADD COMMENTlink modified 3.5 years ago by Devon Ryan89k • written 3.5 years ago by lin.pei2670
0
gravatar for Devon Ryan
3.5 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

I prefer to count orphans as well. Sometimes one of the reads just has crap quality and doesn't align, I see no reason to deflate counts because of that.

ADD COMMENTlink written 3.5 years ago by Devon Ryan89k

Thank you!!

ADD REPLYlink written 3.5 years ago by lin.pei2670
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