Missing Blast fields in outfmt 6

Question

[zgayk]

Hello,

I'm using blast to retrieve 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

Answer 1

[PoGibas]

Is there a newline character after send?

[zgayk]

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

[zgayk]

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