BLAT Results to BED for each Gene
Hi guys,
I have the results from my BLAT search, where I used BLAT to search a list of genes against a reference fasta. I now have a huge list of results and coordinates for each gene against this reference. What I want to do now is to take the best match (or the longest) for each of these genes, and put them into a bed file.
I guess, my question is:
1.) How do I go about finding the "best" match (can I consider the longest the best?) 2.) I was thinking of writing a simple script that looks at all of the gene matches, and takes the line that has the largest match.
Any input would be great!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Finding target for the biologically active compound
written by Pragya •
-
Finding longest CDS for the sequence
written by Sasha •
-
Gene Annotation after EdgeR in R
written by saamar.rajput
-
automatically get description of genes found by blast
written by dp •
-
How to find in frame ORF that overlaps a feature?
written by shjenkins94 •
-
Mapping Gene Models Back to a Reference Genome of Closely Related Species
written by gtasource
-
Coordinates for Gene in Unannotated Reference FASTA
written by gtasource
-
retrieve organism from protein list
written by Assa Yeroslaviz
-
BLAT with cython? Bypassing the IO of BLAT
written by adkhawkins •
-
Is Blat A Good Choice To Find 18Mers In A Custom Fasta File
written by Alex Reynolds
What format is the
blatoutput in? If you had used the default PSL format it should be easy to convert it to BED.