How to get mast meme output as bed format file

[Varsha Sundaresan]

Hi could someone please help me output my mast results in a .bed format? Right now I can only get the matrix format xml and txt files but I would like the genomic locations of the matches with chr start and stop. Thank you!

The meme mast command I used is - mast mast_miniMEME.txt genome.fa -o mastout

The output file contains sections -

SECTION: MOTIF DIAGRAMS 

SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM

-------------                      --------  -------------

chr4                                      8  3381_[+1]_933_[-1]_12892_[-1]_

                                             23386_[+1]_3614_[-1]_6950_[-1]_

                                            

SECTION: ANNOTATED SEQUENCES

3376 TTCGC......

4276 GCAAA.....

                 

The format I wanted is of the format - 

chr start stop

chr4 3376 3390....                              

I was wondering if there is a command line option to get this format directly.

[CharlesEGrant]

It sounds like what you want are the locations of matches to motifs. That's really a more appropriate job for FIMO. MAST's job is to score sequences for overall similarity to a collection of motifs, and only incidentally creates a list of motif matches, not all of which may be reported! This post may be helpful: How does MAST differ from FIMO?

FIMO doesn't produce BED files per se, but it does produce GFF files, and a plain text format that's easily translated to BED.

[Varsha Sundaresan]

I just found out the command to get the bed format was use -hit_list in the command line option with mast. I will try FIMO as well, thank you!