How to deal with gaps in fasta file, because it seems they are illegal characters

[Marja Roslund]

Hi,

I am running picrust2_pipeline.py command, and I get error message illegal character -

I can see that the example fna file does not contain these gaps, however, my representative sequences always contain gaps, for example:

>M01089_38_000000000_CBDCP_1_2103_13851_15011
TAC-GG-AG-GAT--CCG-A-G-C--G-T-T--AT-C-CGG-AT--TT-A-T-T--GG-GT--TT-AAA-GG-GA-GC--

 
>M01089_38_000000000_CBDCP_1_2105_9506_11205
TAC-GT-AG-GGG--GCA-A-G-C--G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-AAA-GG-GA-GC--

What should I do with these gaps? Thank you for your help :)

Cheers,

Marja

[Gavin Douglas]

Hey Marja,

You will need to remove those characters. You can do that with sed for example on the command line:

sed ’s/-//g’ FASTA

Although you would want to make sure that there were no “-“ characters in any headerline. You could check that by running:

grep “>” FASTA | grep “-“ 

Cheers,

Gavin

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