This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Convert BLAT to GFF file?

Does anyone know of a handy script to convert a PSL file from a BLAT alignment to a GFF annotation file? It seems like a PSL has all of the information needed to build a GFF file, but I cannot seem to find a script out there to do the dirty work for me.

blat psl gff alignment annotation
• 4,698 views • link
updated by pengchy pengchy • written by rm16 • rm16

Another alternative method is using Gmap alignment tools with GFF output format

-f, --format=INT               Other format for output (also note the -A and -S options
                                   and other options listed under Output types):
                                   psl (or 1) = PSL (BLAT) format,
                                   gff3_gene (or 2) = GFF3 gene format,
                                   gff3_match_cdna (or 3) = GFF3 cDNA_match format,
                                   gff3_match_est (or 4) = GFF3 EST_match format,
                                   splicesites (or 6) = splicesites output (for GSNAP splicing file),
                                   introns = introns output (for GSNAP splicing file),
                                   map_exons (or 7) = IIT FASTA exon map format,
                                   map_ranges (or 8) = IIT FASTA range map format,
                                   coords (or 9) = coords in table format,
                                   sampe = SAM format (setting paired_read bit in flag),
                                   samse = SAM format (without setting paired_read bit),
                                   bedpe = indels and gaps in BEDPE format
• 0 views • link
written by pengchy pengchy

2 answers

You should have found this (psl2gff.py) in your search.

• 0 views • link
written by GenoMax GenoMax

This works fine.

• 0 views • link
written by opplatek opplatek

Log in to answer this question.

More posts like this