straglr
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Problem with --trf_args
No matter what values I assign to --trf_args, I get this error: straglr.py: error: argument --trf_args: expected 7 arguments
For reference, here is the command I am running
sbj=PBMC_XXXX
bam=/mnt/seq/GRCh38/${sbj}/${sbj}.GRCh38.sorted.bam
fa_ref=/mnt/VNTR/VNTR_gene_strglr/hg38.fa
output=PBMC_XXXX_straglr
loci_bed=/mnt/vntr_region_motifs.e.bed
# Provide the TRF arguments, such as Match, Mismatch, Delta, PM, PI, Minscore, MaxPeriod
trf_args="2 7 7 80 10 50 500"
python /mnt/VNTR/VNTR_gene_strglr/straglr-master/straglr.py $bam $fa_ref $output --loci $loci_bed --debug --trf /home/ilaria99/TRF --trf_args $trf_args