Hi,
I intend to implement multiple binning approaches using Hi-C data for a pipeline, and I'd like to use the same bam file for all of them. Briefly, this bam file has been created with the Arima HiC mapping pipeline, and includes read pairing information.
For metaTOR, I was planning on separately extracting the forward and reverse reads and remove all flag information except for the strand (0 or 16), like so:
samtools view -@ 10 -h -f 0x40 --remove-flags 4079 -b -o fwd.bam aln.bam
samtools view -@ 10 -h -f 0x80 --remove-flags 4079 -b -o rev.bam aln.bam
Is this going to work properly or is there something I am missing? Would it be better for me to directly create a pair files after filtering low quality alignments from the bam file?
Best regards,
Yann
Hi,
I intend to implement multiple binning approaches using Hi-C data for a pipeline, and I'd like to use the same bam file for all of them. Briefly, this bam file has been created with the Arima HiC mapping pipeline, and includes read pairing information.
For metaTOR, I was planning on separately extracting the forward and reverse reads and remove all flag information except for the strand (0 or 16), like so:
Is this going to work properly or is there something I am missing? Would it be better for me to directly create a pair files after filtering low quality alignments from the bam file?
Best regards,
Yann