search

FelixKrueger / SNPsplit

Allele-specific alignment sorting
http://felixkrueger.github.io/SNPsplit/
GNU General Public License v3.0
52 stars 20 forks source link

question regarding the HiC module #23

Closed vivekbhr closed 5 years ago

vivekbhr commented 5 years ago

Hi @FelixKrueger

Could you please tell me a bit about the format of the BAM files that you need in snpsplit for read sorting from HiC data? HiCUP manual is not clear about the output BAM, but I am assuming that

1) It maps the R1 and R1 seperately using bowtie/bowtie2 2) removes invalid HiC pairs 3) Interleaves the R1 and R2 from valid pairs and write the sample1_2.bam, which can be taken by snpsplit

In that case I could in principle just map my R1 and 2 seperately using bowtie2, then interleave the output files, and this should serve as valid input for snpsplit. Am I correct?

Thanks, Vivek

FelixKrueger commented 5 years ago

Hi Vivek,

Yes I think the output from HiCUP is a BAM file where R1 and R2 follow each other in consecutive lines. If you arrive at a similar file by whatever method and specify --hic in SNPsplit, I don't see why it wouldn't work in the very same way.

vivekbhr commented 5 years ago

Hey Felix. So we tested with raw bowtie mapping and it works as long as both reads are mapped and alignments are interleaved. Thanks!

FelixKrueger commented 5 years ago

Excellent! Phil :P