BED to BigBed conversion problem.

Question

[ashkan]

Hi Guys, I am trying to convert BED file to BigBed file using the following command: " bedToBigBed 3_accepted_hits.bed chrom.sizes myBigBed.bb ". the error is: "bedToBigBed: command not found" my bed file and bedToBigBed (downloaded from UCSC) are in the same directory.

who knows how I can solve this problem?

thanks

Answer 1

[Ryan Dale]

Instead of bedToBigBed try typing ./bedToBigBed (with a leading dot and forward slash). See http://www.linfo.org/dot_slash.html for why this is needed.

[ashkan]

@Ryan: I tried and gave this error: "bash: ./bedToBigBed: Permission denied"

[Devon Ryan]

chmod a+x bedToBigBed and then it'll likely work.

[ashkan]

again this error: "bash: ./bedToBigBed: Permission denied"

[GenoMax]

A possibility is that you are working in a normal user account and may need to do sudo chmod a+x ./bedToBigBed in the directory where the file is present.