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a guest Oct 13th, 2019 89 Never
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  1. #!/bin/bash
  2.  
  3. INPUT_FQ=demo_reads.fq
  4. TRANSCRIPTOME="transcriptome.fas"
  5. COUNT_TSV="online_counts.tsv"
  6. COUNT_MONITOR="[ -f $COUNT_TSV ] && ( csvtk -t watch -O sec_dist.pdf -B 100 -f SecCount $COUNT_TSV ; sleep 2)" # script to monitor secondary read count distribution
  7.  
  8. csvtk cat $INPUT_FQ \
  9. | seqkit seq -Q 3 \
  10. | seqkit watch -x -f MeanQual -p 20000 \
  11. | minimap2 -t 20 -K 100k -ax map-ont $TRANSCRIPTOME -  2>/dev/null| samtools view -b \
  12. | seqkit bam  -B 3 -f IsSec -W 4 -x -p 4000 \
  13. | seqkit bam -Q -m 1 -x -p 600000 -c $COUNT_TSV -e "$COUNT_MONITOR" \
  14. | samtools sort -o sorted_aln.bam -
  15. samtools index sorted_aln.bam;
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