hey dude,
I had a sam file which I extracted unmapped reads as unmapped.sam using samtools view, I am going to create a new file.sam containing only the mapped reads and the reads which maps only with a high mapping quality (MAPQ=42), please someone tell me the command I should type in cmd (I'm on Windows). I tried some code but not working...
ok, show us
It means I should first convert unapped.sam to bam then try to high quality mapping?
Hey Pierre, it says that fail to read the header
Sarah, I think you need to be clear with the file formats that you have been using in your question. Do you have a bam file currently or is it a sam file? Do you want to create a sam file containing reads with MAPQ >= 42 or do you want to create a bam file.
Ashutosh I have a sam and I need a filtered sam too, :(