I have an unmasked genome and its repeat file in bed/gff format. I tried to softmask the genome using maskFastaFromBed from bedtools (v2.26), but it doesn't automatically mask the minus strand by taking strand information from the .bed file. There is no -s option to switch on strandedness either (a feature available in getfasta). So basically, the masking is always returned on the + strand and I'm surprised! Does anyone have any ideas or alternative tools to suggest? Example run and output is below.
Chr1 ATTGACAGAAATATCATCACATCTATTCTTTCTCTCCCCTAGTTTAGCAAAT Chr2 GACATATAAATAATAGTGGGAAAGAGACCGGATGAAACCTCAACTGTGGCTTTCATTAACAGATCA
Chr1 0 17 for 1 + Chr2 0 17 rev 1 -
maskFastaFromBed -soft -fi genome.fasta -bed genome.bed -fo genome_softmasked.fasta
Chr1 attgacagaaatatcatCACATCTATTCTTTCTCTCCCCTAGTTTAGCAAAT Chr2 gacatataaataatagtGGGAAAGAGACCGGATGAAACCTCAACTGTGGCTTTCATTAACAGATCA