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ont2d not supported by bwa #108

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afadda1 opened this issue Dec 11, 2023 · 0 comments
Open

ont2d not supported by bwa #108

afadda1 opened this issue Dec 11, 2023 · 0 comments

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@afadda1
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afadda1 commented Dec 11, 2023

Hi,
it seems like bwa mem does not support ont2d reads
/BWA/0.7.7/bwa mem -t1 -x ont2d -M -a /gpfs/software/genomics/HLA-LA_comp/HLA-LA/src/../graphs/PRG_MHC_GRCh38_withIMGT/extendedReferenceGenome/extendedReferenceGenome.fa /R_U.fastq.splitLongReads | /gpfs/software/genomics/SAMtools/1.9/bin/samtools view -@ 0 -Sb - > /PRG38/SIR000174000075/remapped_with_a.bam.unsorted
mem: invalid option -- 'x'
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