Bismark paired-end positions

[mixter]

Hello,

I noticed that Bismark paired-end runs give you an output with start/stop genomic positions only for the first read, but not for its mate.

As the two mates overlap but do not have identical start/stop positions, is there a recommended way to discern the start/stop position of the second read, without having to re-align it to the genome or to its mate?

I'm aware that methylation_extractor takes care of this, but I'd be interested in the full sequence of paired-end runs in addition to the methylation call.

Any suggestions would be greatly appreciated!

[fkrueger]

Hello,

I noticed that Bismark paired-end runs give you an output with start/stop genomic positions only for the first read, but not for its mate.

As the two mates overlap but do not have identical start/stop positions, is there a recommended way to discern the start/stop position of the second read, without having to re-align it to the genome or to its mate?

I'm aware that methylation_extractor takes care of this, but I'd be interested in the full sequence of paired-end runs in addition to the methylation call.

Any suggestions would be greatly appreciated!

Hi Mixter,

the older output format (now called vanilla) does not report the start and end positions of the first read but of the the read pair as a whole. If you want to get the individual start end positions of each read it would be start + length (read1) or end - length(read2)+1.

The latest versions of Bismark (0.6.x) can also output SAM format, in which every read is reported on a separate line, so it is quicker to see where each of the reads was aligned. And just for the record, reads that overlap perfectly are not considered a valid alignment by Bowtie (this is intentional) and are thus not reported at all.

Hope this helps,
Felix