barrnap

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enhancement: add option to slice input contigs

1

Torsten- An idea for enhancement: would be great to have an option for barrnap to write fasta file(s) containing just the detected rRNA sequences, i.e. to slice the input contigs...

jbadomics

Add RnaseP and SRP genes

2

@tseemann, if possible I'd like to add some additional genes to barrnap. Would this be suitable? I've noticed that `bin/barrnap` appears to need the lengths of these genes, how should...

michaelbarton

See #2 Closes #12

sjackman

I got this bug when using the `--outseq` : ``` [barrnap] Running: bedtools getfasta -s -name+ -fo 'out.fa' -fi '/tmp/DCK1ZXW9lo' -bed '/tmp/C6qa9HAUtf' *****ERROR: Unrecognized parameter: -name+ ***** ``` The problem...

johanzi

SILVA version?

1

Sorry, if it is mentioned somewhere. But I could not find which Version of SILVA was used for the creation of the HMM. Sincerely Thomas Dost

Unaimend

update DBs using RFAM 15.9 & SILVA 138.1

1

This also removes the commercial use restriction from the bundled databases as the new SILVA release is now CC-BY 4.0.

mr-c

My fasta file is definitely valid, but get this error. Command: nhmmer --cpu 12 -E 1e-06 --w_length 3878 -o /dev/null --tblout /dev/stdout '/g/data/nm31/bin/barrnap/bin/../db/euk.hmm' 'nothofagus_assembly.fasta' [barrnap] ERROR: nhmmer failed to run...

theo-allnutt-bioinformatics