Could someone please help with the exact syntax to make bam file from fastQ RNA-seq ion torrent with BBmap installed on windows 7 (command prompt). I've installed BBmap on Windows 7 but struggling to understand how to run the tool.
I found a post that describes this line but it's not clear how to provide the reference for the alignment?
I've tried indexing the reference but it's not working:
- I navigated to bbmap folder where bbmap.sh and hg19.fasta are located and ran the following command: C:\tesm\bbmap>bbmap.sh ref=hg19.fasta and 'Open With' window popped up. What am I doing wrong?