Hi,
I have created my bowtie2 indexes but they cant seem to be located when I run my code.
file=$"S1_7"
ribosomal="/lustre7/home/lustre3/mas/mm10/Sequence/AbundantSequences/musRibosomal"
singularity exec /usr/local/biotools/b/bowtie2:2.3.3.1--py36pl5.22.0_0 bowtie2 -p 6 --un-conc ${file}_noribo.fq --al-conc ${file}_ribo.fq -x $ribosomal -1 ${file}_R1_3.fastq -2 ${file}_R2_3.fastq
(ERR): "/lustre7/home/lustre3/mas/mm10/Sequence/AbundantSequences/musRibosomal" does not exist or is not a Bowtie 2 index
Exiting now ...
Is there anything I am doing wrong here?
Thanks in advance.
The error is pretty obvious. What is the name of the index files? Can you go into the index directory and show the output of
ls
?Thank you, I'm completely new to this field. Here is the output of ls. musRibosomal.fa rRNA.1.bt2 rRNA.2.bt2 rRNA.3.bt2 rRNA.4.bt2 rRNA.rev.1.bt2 rRNA.rev.2.bt2