Samtools on Mac: how to use??

[Pennaki]

Hello everyone!!

I'm very new to bioinformatics, trying to index a .bam file on my mac using samtools, so my question might be very silly. I installed samtools yesterday, tried to convert a .sam to .bam and it worked. However, today I got a .bam file which I tried to index it using the

index test1.bam

but I keep getting this:

-bash: index: command not found

What am I doing wrong?!

Thank u!

[chadn737]

did you put "samtools" before "index"?

Your command should be:

$ samtools index test1.bam

[Pennaki]

I did, and I'm getting this:

-bash: samtools: command not found

[chadn737]

Are you sure you have samtools installed correctly?

[chadn737]

How did you get samtools to convert a sam to a bam?

[Pennaki]

By typing:

$samtools view -bS test1.sam > test1.bam

:/

[Pennaki]

Got it! It had to do with the path or something, I typed ./samtools instead of samtools and it worked!!