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Missing Blast fields in outfmt 6
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4.2 years ago
zgayk • 90
United States

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 • 1.7k views
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13 months ago
PoGibas 4.8k
Vilnius

Is there a newline character after send?

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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

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

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