Discordant reads output

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Prachiti Prabhu

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Dec 18, 2021, 10:28:58 PM12/18/21
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Hello all,
For my experiment, I wanted to specifically view the discordant reads (read pairs that are too far apart, read pairs that are in the incorrect orientation or read pairs where mates map to different chromosomes). However, I have noticed that such read go unmapped. Is there any way to map and output these discordant reads? And if there is, are they flagged in any way?

Thanks,
Prachiti

Alexander Dobin

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Dec 18, 2021, 10:36:45 PM12/18/21
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Hi Prachiti,

if you want to output discordant pairs, you can reduce --outFilterScoreMinOverLread and --outFilterMatchNminOverLread to below 0.5, e.g.:
--outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4
Such alignments will have 0x2, 0x4 and 0x8 bits *not* set in the FLAG field of the SAM/BAM files.

Cheers
Alex

Prachiti Prabhu

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Dec 21, 2021, 7:24:33 PM12/21/21
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Thank you, Alex. I appreciate you taking the time to reply. I will try that out and get back to you if I have further questions.

Best,
Prachiti
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