question regading the isoseq cluster2 parameters

[lyj95618]

Hello,

I am curious if it is possible to alter the cutoff of the 5', 3' overhang for isoseq cluster2.

I know the current cutoffs are <100bp 5' overhang, <30bp 3' overhang, <10bp gaps. Is it possible to loosen the cutoff to something like < 200bp 5' overhang.

Thanks! Laur

[armintoepfer]

Sure, try --overhang-5 200

[lyj95618]

thanks for the quick reply!

I believe I can do a similar thing if I want to alter the 3' cutoff. It would be great if these options are listed in the help page. when I run isoseq cluster2, I only see the following:

Usage:
  isoseq cluster2 [options] <flnc.bam|xml|fofn> <transcripts.bam>

  flnc.bam|xml|fofn  STR   Input flnc BAM, ConsensusReadSet XML, or FOFN
  transcripts.bam    STR   Output transcripts BAM

  --singletons             Output FLNCs that could not be clustered.
  --sort-threads     INT   Number of sorting threads per BAM file. Equivalent to open file handles per BAM.
                           Defaults to -j. [0]
  --write-bam        STR   Write annotated BAM file.

  -h,--help                Show this help and exit.
  --version                Show application version and exit.
  -j,--num-threads   INT   Number of threads to use, 0 means autodetection. [0]
  --log-level        STR   Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL). [WARN]
  --log-file         FILE  Log to a file, instead of stderr.

Thanks again for the help! Laur