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

[huan]

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

[bowhan]

To generate the summary plot "fulllength_nonchimeric_readlength_hist.png", you will need to run the script "isoseq_classify_report.py", such as

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

[huan]

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

[lingling huang]

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!

[Magdoll]

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