Filteration of uniquely mapped reads
Hello
I have BAM-full file with reads mapped to “human and mouse” chromosome file. Now I would like to extract reads mapped only to “mouse” (means not mapped to human chromosome”. This is the protocol I am using :
- From BAM-full, extract reads mapped to Mouse chromosome and convert to fastq1
- From BAM-full, extract reads mapped to Human chromosome and convert to fastq2
- Extract read ids from both fastq1 and fastq2 and identified non-overlapped “reads” ids from fastq1
I would like to know if there is samtool command or software to apply these filtrations steps ?
Thanks alot in advance
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