2019-07-29 iso-seq3

isoseq3 - De Novo Transcript Reconstruction

Usage:
  isoseq3 <tool>

Options:
  -h, --help   Output this help.
  --version    Output version info.

Tools:
    cluster    Cluster CCS reads and generate unpolished transcripts (CCS to UNPOLISHED)
    polish     Polish transcripts using subreads (UNPOLISHED to POLISHED)
    summarize  Create barcode overview from transcripts (POLISHED to CSV)

Examples:
  isoseq3 cluster movie.consensusreadset.xml unpolished.bam
  isoseq3 polish unpolished.bam movie.subreadset.xml polished.bam
  isoseq3 summarize polished.bam summary.csv

Typical workflow:
   1. Generate consensus sequences from your raw subread data
      $ ccs movie.subreads.bam movie.ccs.bam --noPolish --minPasses 1

ccs教程链接 ：

   2. Primer removal and demultiplexing
      $ cat primers.fasta
        >primer_5p
        AAGCAGTGGTATCAACGCAGAGTACATGGGG
        >primer_3p
        AAGCAGTGGTATCAACGCAGAGTAC
      $ lima movie.ccs.bam primers.fasta demux.ccs.bam --isoseq --no-pbi

lima教程链接：

   3. Cluster consensus sequences to generate unpolished transcripts
      $ isoseq3 cluster demux.P5--P3.bam unpolished.bam --verbose

   4. Polish transcripts using subreads
      $ isoseq3 polish unpolished.bam movie.subreads.bam polished.bam

结果如何呢

isoseq3 cluster demux.P5--P3.bam unpolished.bam --verbose
isoseq3 polish unpolished.bam movie.subreads.bam polished.bam