Closed vivekbhr closed 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.
Hey Felix. So we tested with raw bowtie mapping and it works as long as both reads are mapped and alignments are interleaved. Thanks!
Excellent! Phil :P
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 snpsplitIn 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