bwa-meth unrecognized reference name during sam_parse

bwa-meth unrecognized reference name during sam_parse

0

Dear all,

I have some Enzymatic methyl sequencing data that I am trying to align using bwa-meth (github.com/brentp/bwa-meth). However, I am encountering the following issue in parsing of the sam file that the aligner is generating when I try to convert the sam file to a bam file.

[W::sam_parse1] unrecognized reference name ""; treated as unmapped

This is the first time for me using bwa-meth tool and I am not able to solve this issue. I am running the following command as suggesting on the GitHub page mentioned above.

bwameth.py --reference ref_genome.fa Sample1_1.fastq.gz Sample1_2.fastq.gz -t 7 | samtools view -b - > sample1.bam

Any help is appreciated.

Thank you.


EM-seq


Methyl-seq


alignment


bwa-meth

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