I am new with nanopore and I am following a script to analyse 16S sequencing from Nanopore raw data, when I tried to remove the chimeras from the all data with a loop:
time(for i in $1*nanofilt.fastq
do
minimap2 -x ava-ont -g 500 -t 12 $i $i > ${i%%.*}.paf
yacrd -i ${i%%.*}.paf -o ${i%%.*}.yacrd -c 4 -n 0.4 scrubb -i $i -o ${i%%.*}.scrubb.fastq
rm ${i%%.*}.paf
done)
I do not obtained the expected files, but I do not have any error, so I can not know what is the problem. I am using 20.04 version of ubuntu. Could be an syntax error or compatibility?
I tried the script sample by sample:
minimap2 -x ava-ont -g 500 -t number_of_threads input_file-porechop-nanofilt.fastq input_file-porechop-nanofilt.fastq > input_file-porechop-nanofilt.paf
yacrd -i input_file-porechop-nanofilt.paf -o input_file-porechop-nanofilt.yacrd -c 4 -n 0.4 scrubb -i input_file-porechop-nanofilt.fastq -o input_file-porechop-nanofilt.scrubb.fastq
rm *.paf
But I need to add all samples at time, and for this reason I use the loop.
Thanks in advance