Question: Missing Blast fields in outfmt 6
0
gravatar for zgayk
3.3 years ago by
zgayk90
United States
zgayk90 wrote:

Hello,

I'm using blast to retreive sequence matches and I want the subject start and end coordinates. But, I notice that although the subject start returns a column, there is no column for the subject end field.

Here is the code I used:

blastn -query  Gaviaimmerheader.fasta  -db Gallus_gallus.Galgal4.cds.all.fa -task blastn -dust no -outfmt "6 qseqid sseqid  length qstart qend sstart send
sallgi qseq sseq  evalue" -evalue 1e-6  -num_alignments 1 -max_hsps 5 -out outputgallus8.blast.txt

If anyone knows why the send field is entirely absent, let me know.

Thanks,

Zach

blast • 1.4k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by zgayk90
0
gravatar for PoGibas
3.3 years ago by
PoGibas4.7k
Vilnius
PoGibas4.7k wrote:

Is there a newline character after send?

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by PoGibas4.7k

I don't believe so. I checked and didn't see one there. It could also be displayed like this:

blastn -query  Gaviaimmerheader.fasta  -db Gallus_gallus.Galgal4.cds.all.fa -task blastn -dust no -outfmt "6 qseqid sseqid pident length qstart qend sstart send sallgi evalue qseq sseq" -evalue 1e-6  -num_alignments 1 -max_hsps 5 -out outputgallus8.blast.txt

 

ADD REPLYlink written 3.3 years ago by zgayk90

Thank you, I figured out what was wrong. Blast wasn't reading all the fields becuase the code wasn't all on one line.

ADD REPLYlink written 3.3 years ago by zgayk90
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: 1483 users visited in the last hour