I am testing the em-seq.nf workflow and I am running into the following issue:
I used bwameth.py to perform c2t conversion and indexed the reference genome. It generates forward and reverse reference sequences and names them fchr1, rchr1, fchr2 , rchr2… etc. The problem is that my aligned bam files contain mapping to the forward and reverse reference sequences. The later step in the pipeline (select_human_reads using sambamba) queries for chr1,chr2,chr3 for post processing and it is failing due to the difference in chromosome names in my aligned bam file (rchr1,fchr1 etc).
Let me know if you need more information.
Thanks,
Meg
Hi,
I am testing the em-seq.nf workflow and I am running into the following issue:
I used bwameth.py to perform c2t conversion and indexed the reference genome. It generates forward and reverse reference sequences and names them fchr1, rchr1, fchr2 , rchr2… etc. The problem is that my aligned bam files contain mapping to the forward and reverse reference sequences. The later step in the pipeline (select_human_reads using sambamba) queries for chr1,chr2,chr3 for post processing and it is failing due to the difference in chromosome names in my aligned bam file (rchr1,fchr1 etc).
Let me know if you need more information. Thanks, Meg