sh 在所有k长度和文件中运行telseq。 ＃分析

Posted 2021-05-07

# Add header line
echo -e "file\tk\tflag\t`telseq -h`" > ../telseq_WI.tsv
# Calculate!
parallel --gnu --verbose "samtools view -F {3} -h {2} | \
awk '/^@/  { print } {if (length(\$10) > 80) { print }}'  | \
samtools view -b - | telseq -z TTAGGC -H -k {1} - | \
awk -v s={2} -v k={1} -v flag={3} '{ print s \"\t\" k \"\t\" flag \"\t\" \$0}' | \
egrep -v '\[-\]|BAMs' >> ../telseq_WI.tsv" ::: 7 ::: `ls *.bai | sed 's/.bai//g' | grep -v 'sorted' | grep -v 'SRR'` ::: 0x0400 0x0000