So I have my .sam file aligned from Bowtie2 and have dowloaded SAMtools and BCFtools. I added SAMtools to PATH using:
export PATH:$PATH:#path/#to/SAMtools (I renamed whatever the samtools name was to just "SAMtools"
Now, the instructions say that to convert from .sam to .bam, you simply type:
samtools view -bS filename.SAM > filename.BAM
However, no matter what I try I keep getting "samtools: command not found"
What am I doing wrong?
export PATH:$PATH:#path/#to/SAMtools (I renamed whatever the samtools name was to just "SAMtools"
Now, the instructions say that to convert from .sam to .bam, you simply type:
samtools view -bS filename.SAM > filename.BAM
However, no matter what I try I keep getting "samtools: command not found"
What am I doing wrong?
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