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This may be a truly trivial question but I must ask it...
So, I'm aligning some mouse reads to the mouse genome using GSnap. I've used GSnap before for human rna-seq data. So, I assumed things would be pretty similar. (Of course I've got the necessary reference files and such.) So, I went to run it using these commands: gsnap --gunzip -d Mouse --format=sam --nthreads=12 --sam-multiple-primaries --kmer=15 --basesize=12 -N 1 -B 4 MouseTest_S1_L001_R1_001.fastq.gz MouseTest_S1_L001_R2_001.fastq.gz
And then I got this: This is a large genome of more than 2^32 billion bp.
You should run gsnapl instead.
So, yes, I ran gsnapl, and it ran with no errors. But it didn't take long at all. Literally, it is the quickness that is making me nervous. Does anyone have any experience with this???
So, I'm aligning some mouse reads to the mouse genome using GSnap. I've used GSnap before for human rna-seq data. So, I assumed things would be pretty similar. (Of course I've got the necessary reference files and such.) So, I went to run it using these commands: gsnap --gunzip -d Mouse --format=sam --nthreads=12 --sam-multiple-primaries --kmer=15 --basesize=12 -N 1 -B 4 MouseTest_S1_L001_R1_001.fastq.gz MouseTest_S1_L001_R2_001.fastq.gz
And then I got this: This is a large genome of more than 2^32 billion bp.
You should run gsnapl instead.
So, yes, I ran gsnapl, and it ran with no errors. But it didn't take long at all. Literally, it is the quickness that is making me nervous. Does anyone have any experience with this???
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