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  • number of reads

    Hi users,
    I want to know number of reads from Illumina fastq (.txt file), number of reads that are aligned by bwa (from bam files), number of reads that are aligned in target genes (genes enrichment sequencing).

    Someone could help me?
    Thanx a lot!!!
    ME

  • #2
    What programming languages do you know (if any)? Or are you hoping for command line tool recommendations?

    Comment


    • #3
      I'm trying samtools idxstats for mapped reads and this command for reads in target genes
      > samtools view file.bam | awk '$3=="chr" && $4>=start_target_genes && $8<=end_target genes' > reads
      > wc -l reads

      Is this ok?

      Comment

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