I have a 151bp sequence which I want to see if part or all of it would map to other regions of the mouse genome. I have currently tried the following:
ref=/path/to/Ensembl_index_GTF_Mus_musculus_GRCm38_87/Mus_musculus.GRCm38.dna.primary_assembly.fa in=/path/to/Zeb2os_Overlap/Zeb2os_overlap_with_Zeb2.fa out=mapped_$(date +"%Y%m%dT%H%M").txt
bbmap.sh ref=$ref in=$in outm=$out minratio=0.4 minid=0.4
Is this the correct way to do this?
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I have a 151bp sequence which I want to see if part or all of it would map to other regions of the mouse genome. I have currently tried the following:
ref=/path/to/Ensembl_index_GTF_Mus_musculus_GRCm38_87/Mus_musculus.GRCm38.dna.primary_assembly.fa
in=/path/to/Zeb2os_Overlap/Zeb2os_overlap_with_Zeb2.fa
out=mapped_$(date +"%Y%m%dT%H%M").txt
bbmap.sh ref=$ref in=$in outm=$out minratio=0.4 minid=0.4
Is this the correct way to do this?