bsmap /methratio/ paired end mode and unpaired aligned reads

Question

[francesca3]

Hi everyone. Anyone knows if, following paired-end alignement with bsmap, methratio.py will use also the unpaired mapped reads to extract the ratio or just the properly paired?

Thanks

Francesca

Answer 1

[sklages]

The default is to use all mapped data, if you want methratio.py to use only properly paired reads, use --pair parameter.

 $ ./methratio.py -h
Usage: methratio.py [options] BSMAP_MAPPING_FILES
[..]
  -u, --unique          process only unique mappings/pairs.
  -p, --pair            process only properly paired mappings.
[..]

[francesca3]

Thanks, one more question. Since I noticed that in my experiment (but I think it happens all the times), there are some "mates" that mapped on different chromosomes, do you know how these reads are treated?

Thanks a lot

Francesca