Rafail Tasakis

Dear Ernesto, I’ve tried what you pointed out on your last response. I got back the pysam 0.13 and tried to run the REDItoolDnaRna_1.1.py you provided me with last time. Unfortunately it doesn’t work again. My input is: python REDItoolDnaRna_1.1.py -i /Users/tasakis/Documents/Moor_BAM/UnsortedBAMs/SRR5280291Aligned.out.bam \ -I /Users/tasakis/Documents/Moor_BAM/SortedBAMs/SRR5280291Aligned.sortedByCoord.out.bam \ -f /Users/tasakis/Documents/Mus_musculus.GRCm38.dna_sm.toplevel.fa \ -o /Users/tasakis/Desktop/TEST...

Dear Ernesto, thank you very much for getting back to me. I tried as you said. Also made sure that the fa.fai file of the reference genome is in the same directory with that. My input command it this now: REDItoolDnaRna.py -i /Users/tasakis/Documents/Moor_BAM/UnsortedBAMs/SRR5280291Aligned.out.bam \ -I /Users/tasakis/Documents/Moor_BAM/SortedBAMs/SRR5280291Aligned.sortedByCoord.out.bam \ -f /Users/tasakis/Documents/mm10.fa \ -o /Users/tasakis/Desktop/TEST -F RUN However I still ge the same error....

Fasta file not found, while I provide it