pipeline: run repeatmasker on chrY contigs

marschall-lab / project-male-assembly

HGSVC SIG: targeted chromsome Y assembly

MIT License

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pipeline: run repeatmasker on chrY contigs #4

Closed ptrebert closed 2 years ago

ptrebert commented 2 years ago

run with default parameters

ptrebert commented 2 years ago

it evades me why so many tools still use Stone Age limits on identifier names, sequence lengths and so on...

Fasta file contains a sequence identifier which is too long ( max id length = 50 )

workaround: run repmask on original tig names, and rename later...

ptrebert commented 2 years ago

@pilleh which output besides the tabular output (.out) of the repeatmasker runs do you need (I'll keep everything by default, just not to clutter the Globus share)

N-masked FASTA sequence
fasta.cat.gz output
report summary .tbl

pilleh commented 2 years ago

@ptrebert The repeatmasker results in the first instance will be used by Arthur and Mark&Miriam. To be on the safe side, I would add all these to Globus since I'm not 100% sure what they need.

ptrebert commented 2 years ago

done - results are automatically available from now on. RepeatMasker is run with default settings in -s / slow search mode.

pilleh commented 2 years ago

@ptrebert You are über cool! thanks a lot!