Comments (2)
yes, those are just chunks of reads that bwa mem operates on, you should see many of them.
from bwa-meth.
Hi,
Thanks for the quick reply! I actually have another question following this:
My original code is to pipe this output to samtools sort
bwameth.py --threads 12 --reference "genome.fa"\
"FASTQ/211029_1_FZ_WGBS_HOIK_p35_rep1_S1_L001_R1_001_MM_1.fastq.gz" \
"FASTQ/211029_1_FZ_WGBS_HOIK_p35_rep1_S1_L001_R2_001_MM_1.fastq.gz" \
2> bwameth/logs/211029_1_FZ_WGBS_HOIK_p35_rep1_S1_L001.map_reads.err | \
samtools sort -T "$MYTEMP"/211029_1_FZ_WGBS_HOIK_p35_rep1_S1_L001 -m 3G -@ 4 \
-o "bwameth/211029_1_FZ_WGBS_HOIK_p35_rep1_S1_L001.bam" \
2>> bwameth/logs/211029_1_FZ_WGBS_HOIK_p35_rep1_S1_L001.map_reads.err
But here I get error [W::sam_parse1] unrecognized reference name ""; treated as unmapped
A similar issue was mentioned here and I also checked that
$ head genome.fa.bwameth.c2t
>rchr1 1
Could this cause the unrecognised reference? Thanks for the help!
from bwa-meth.
Related Issues (20)
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from bwa-meth.