I ran the code python /dir/bs_seeker2-build.py -f MyGenome -d /out/dir/ --aligner=bowtie2 -p /u/local/apps/bowtie2/2.2.9
In MyGenome there is a contig named Seg3751.2; however, the index has Seg3751_2 instead of Seg3751.2. Did I do anything wrong that resulted in this name change? When I tried to use MethylDackle mbias on my bam files I got an error saying 'Seg3751_2 could not be found in the reference genome'. So I'd like to keep the names consistent. What is the best course of action for me? Can I just rename Seg3751_2.data to Seg3751.2.data and do the mapping again?
Hello,
I ran the code
python /dir/bs_seeker2-build.py -f MyGenome -d /out/dir/ --aligner=bowtie2 -p /u/local/apps/bowtie2/2.2.9
In MyGenome there is a contig named Seg3751.2; however, the index has Seg3751_2 instead of Seg3751.2. Did I do anything wrong that resulted in this name change? When I tried to useMethylDackle mbias
on my bam files I got an error saying 'Seg3751_2 could not be found in the reference genome'. So I'd like to keep the names consistent. What is the best course of action for me? Can I just rename Seg3751_2.data to Seg3751.2.data and do the mapping again?Thank you!