--max_fuzzy_junction=0

[abayega]

Hi,

is it okay to run collapse_isoforms_by_sam.py with --max_fuzzy_junction set to 0 (zero)?

Thanks
A

[Magdoll]

Yes, you can run it with --max_fuzzy_junction=0. You may notice that there are more unique transcripts being declared at the end of the collapse step, even transcripts where they only differ 1 or 2 bp at the junctions, as residual errors in HQ isoforms, though rare, can occasionally cause alignment differences.

You can use the summrize scripts here to look at the differences of collapse results later.

[abayega]

Thank you Magdoll, is there any hope of making this script general so that it can be used for any full-length cDNA seq? I realised that when --max_fuzzy_junction>0 the collapse_isoforms_by_sam.py script starts to prob the read names and these will have to be PacBio format otherwise it throws a list index out of range error.

[Magdoll]

Hi @abayega ,
I just answered this question in Cogent issue 13.

You can hack the sequence ID using the short python snippet provided there.

I'll consider allowing for generic IDs for the collapse script in the future.

--Liz

[abayega]

Great, thank you for the help. I will try it out...

[abayega]

Ooops, I

[abayega]

Sorry, I meant to just comment, you can close this whenever you want