Mapping only one end of paired end reads

Lisle Mose

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Jun 10, 2016, 2:59:55 PM6/10/16

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Hi,

For paired end mapping, STAR appears to either map both reads or leave both reads unmapped.

In cases where one of the reads maps cleanly, but the other does not could the mapped read be output while its pair is still marked unmapped?

Additionally in these cases, it would be useful to have the unmapped end assigned to its pair's coordinates as is currently done by bwa-mem.

Thanks,

Lisle

Alexander Dobin

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Jun 15, 2016, 12:43:04 PM6/15/16

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Hi Lisle,

you could get single-end alignments by reducing both --outFilterScoreMinOverLread --outFilterMatchNminOverLread to below 0.5, say to 0.4.

These parameters control the minimum read length normalized to the total read length (sum of the mates).

To output the unmapped read, you will need to use --outSAMunmapped Within , the unmapped mate will have the coordinate of the mapped one according to the standard SAM rules.

Cheers

Alex

Lisle Mose

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Jun 19, 2016, 4:42:51 PM6/19/16

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Thanks, this looks like it should work great! I will try it out.

Lisle Mose

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Nov 28, 2016, 5:44:08 AM11/28/16

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Hi,

I am finally getting around to using this in practice. Unmapped reads are output quite nicely when using the --outFilterScoreMinOverLread --outFilterMatchNminOverLread params. However, the coordinates for the unmapped read appear to be unset.

Thanks,

Lisle

Alexander Dobin

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Nov 28, 2016, 3:03:34 PM11/28/16

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Hi Lisle,

not sure I am following your question - if the reads are unmapped, their coordinates cannot be set, can they?