FIMO outputs only Chr1 hits

Ran the following fimo command with a meme PWM on a fasta file of about 10,000 sequences and for some reason it only output hits that map to the 1st chromosome in mm10? Any ideas? Thanks!

fimo /sonas-hs/hpc_norepl/home/MA0212.1.meme /sonas-hs/hpc_norepl/home/resOrderedFem.fa

fimo meme motif

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updated 8.6 years ago by Satyajeet Khare

• written 8.6 years ago by rbronste

I think FIMO is not able to go beyond Chr1 due to default parameters. Try playing with --max-stored-scores and --thresh parameters.

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written 8.6 years ago by Satyajeet Khare

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