Question: Blastn .XML to FASTA
0
gravatar for baurumon
13 days ago by
baurumon10
Norway
baurumon10 wrote:

I have run this command:

blastn -query work.fa -task blastn -db nr -out out.XML -outfmt 5 -evalue 1e-10 -word_size 4 -num_alignments 1 -num_threads 15

enter image description here

Could you please help me to convert this .xml file to fasta??

Thanks in advance

alignment • 95 views
ADD COMMENTlink modified 13 days ago by ATpoint21k • written 13 days ago by baurumon10
2

@Pierre has a solution posted here: Convert XML file to FASTA

You are in general best off using tab delmited output formats since they are are easier to parse. You will then need to get the fasta sequence for the parsed identifiers using blastdbcmd as one option.

ADD REPLYlink modified 13 days ago • written 13 days ago by genomax70k

thank you for the suggestion

ADD REPLYlink modified 12 days ago • written 12 days ago by baurumon10
1

You better do not use imggmi as image hoster, it does not behave well on Biostars. Better use something like Imgur.

ADD REPLYlink modified 13 days ago • written 13 days ago by ATpoint21k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1567 users visited in the last hour