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Old 01-28-2014, 06:38 PM   #1
witty
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Default read counts from samtools idxstats

Hi,

I want to get the read counts for gene expression analysis. I used "samtools idxstats <bam file>" and got the four columns of "contig ID, read length, #mapped reads and # unmapped reads".

My question is I should use #mapped reads(the third column) or (#mapped reads + # unmapped reads)/2 as the raw reads count?

Thank you in advance!
Victoria
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Old 01-29-2014, 03:49 AM   #2
TiborNagy
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Raw read count = mapped reads + unmapped reads
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Old 01-30-2014, 08:14 AM   #3
witty
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Thank you for the response. Alternatively, this adding value divided by two also makes sense, in this case the read counts are the fragments.
I am not sure which result is from the htseq-count, which is generally used as the input for differential gene expression.

THanks!
Victoria
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Old 01-30-2014, 10:35 AM   #4
dpryan
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htseq-count doesn't count multimappers, so the "total reads" that it would report for something and that reported by samtools idxstats may not be very closely related.
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