Question: Genome Annotation Output Files Naming
0
gravatar for Fid_o
10 months ago by
Fid_o20
Fid_o20 wrote:

I ran this annotation command: for k in *.fasta; do prokka $k --outdir "$k".prokka.output; echo $k; done on hundreds of assembled sequences. Each sequence annotation output produced a folder named "sequence_name.prokka.output" but the actual files in the folders were named according to the date e.g. "PROKKA_03062020.gff" for all the folders.

Now I want the actual output be named with the actual FASTA file ID. Example: sequence ID of D02502 should be like this: "PROKKA_D02502.gff"

What do I add (or remove) from the code above?

annotation genome • 497 views
ADD COMMENTlink modified 10 months ago by Mensur Dlakic8.2k • written 10 months ago by Fid_o20
3
gravatar for Mensur Dlakic
10 months ago by
Mensur Dlakic8.2k
USA
Mensur Dlakic8.2k wrote:
for k in *.fasta; do prokka $k --outdir "$k".prokka.output --prefix PROKKA_$k; echo $k; done
ADD COMMENTlink written 10 months ago by Mensur Dlakic8.2k

Thank you sooooo much Mensur Dlakic.

I am learning Bioinformatics and your help is great.

ADD REPLYlink written 10 months ago by Fid_o20

Is there a way to put all prokka output from all fasta files in one folder rather than the traditional output (one folder for the output of each fasta)?

ADD REPLYlink written 18 days ago by Ahmed Ezat El Zowalaty0
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