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  • How can I get the report by using SMRT command-line version?

    Now I have RS_IsoSeq command-line installed, and it works well for filter(getting reads of insert) classify(Getting full length reads) ,Isoform level clustering (ICE and Quiver),but how can I get the similar analysis report generated by SMRT Portal version with both statstic information and plot?

    In addition, how can I evaluate the quality of my rawdata(Quality Control)? Something like whether the data volume is enough(full passes?SMWs?),the quality of each reads(reads of insert accuracy?Q30?cluster reads accuracy?). Is there any software or script can do this?

    Thanks,
    huan
    happy

  • #2
    To generate the summary plot "fulllength_nonchimeric_readlength_hist.png", you will need to run the script "isoseq_classify_report.py", such as
    Code:
    mkdir -p report  && \
    isoseq_classify_report.py \
        isoseq_flnc.fasta  # output from pbtranscript.py classify
        isoseq.classify_summary.txt  # output from pbtranscript.py classify, it also contains the summary information
        output.json  # output json
        -o report  # output folder, need to exist

    Comment


    • #3
      @bowhan Thanks very much! It helps a lotO(∩_∩)O~
      happy

      Comment


      • #4
        Originally posted by huan View Post

        In addition, how can I evaluate the quality of my rawdata(Quality Control)? Something like whether the data volume is enough(full passes?SMWs?),the quality of each reads(reads of insert accuracy?Q30?cluster reads accuracy?). Is there any software or script can do this?

        Thanks,
        huan
        Hi, how do you solve this problem? Could you provide some advice or a link?Thanks!

        Comment


        • #5
          Hi,

          The simplest thing may be to run "RS_subreads" protocol in SMRTPortal. It gives you:

          # of P1 ZMWs in the "Loading" tab
          Polymerase (raw) read quality in the "Filtering" tab
          Mean subread length and total subread base in the "Subread filtering" tab

          You can also download the filtered subreads as a fasta file. That will give you further information about each subread and since the subread sequence IDs tell you which ZMW it is from (each ZMW can generate 0, 1, or more subreads), it gives you a sense of how many passes you are getting per ZMW.

          Hope this helps.

          --Liz

          Comment

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