bamRemoveDuplicates

unread,

Oct 4, 2017, 11:25:44 PM10/4/17

to rna-star

Hi Alex,

How does --bamRemoveDuplicatesType work? Does it have to happen on both read1 and read2 (for paired end) to count as a duplicate?

Thanks,

Olivia

unread,

Oct 5, 2017, 11:34:04 AM10/5/17

to rna-star

Hi Olivia,

duplicates are called if the coordinates of both mates and their CIGARs have to coincide. The soft-clipped ends are extended for comparison.

Cheers

Alex

unread,

Oct 12, 2017, 5:48:30 PM10/12/17

to rna-star

Thanks, Alex,

How do you choose which read to keep? Is it by quality or is it random?

Olivia

unread,

Oct 13, 2017, 11:00:28 AM10/13/17

to rna-star

Hi Olivia,

STAR keeps the read with the best alignment score (AS tag in SAM), i.e. the reads with the min number of mismatches is recorded.

Quality Scores are not taken into account, unlike Picard and samtools. If you are calling variants, you may want to choose by QS.