Scripts

mods_from_bams

If you happen to have BAM files with modifications already encoded in them and just want to process them with modPhred all you need to do is:

  • make new directory ie mods_from_bams/CC.raw_1x

  • copy modPhred.pkl there (it stores info about mods that are present in BAMs)

rsync -av modPhred/raw_1x.m6A/modPhred.pkl mods_from_bams/CC.raw_1x

  • prepare your BAM files in this output dir - BAM files have to be in mods_from_bams/CC.raw_1x/minimap2

  • and run the script

~/src/modPhred/src/mods_from_bams.py -o mods_from_bams/CC.raw_1x \
   -i mods_from_bams/CC.raw_1x/minimap2/*.bam -f ~/cluster/rna_mods/ref/curlcake.fa