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!
I have no idea what a mast meme result looks like, so perhaps you could add an example of what you have and an example of what you would like to obtain.
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]_
SECTION: ANNOTATED SEQUENCES
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.
And those sections look always the same? Multiple sections per file, always the same number of lines with information in the same locations?
Yes, multiple sections and same number of columns.
Can you show some more output to make it completely clear? Perhaps in a github gist
@WouterDeCoster, I just found out the command to get the bed format was -hit_list, thank you anyways!
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