I am planning to run hisat2 on my multiple paired-end samples (>20). Hence, I tried to do the test run as per ftp://ccb.jhu.edu/pub/RNAseq_protocol/ and ran
./rnaseq_pipeline.sh out after editing
rnaseq_pipeline.config.sh. I am getting the following error:
[2017-10-10 11:00:44] #> START: ./rnaseq_pipeline.sh out [2017-10-10 11:00:44] Processing sample: /chrX_data/samples/ERR188044_chrX [2017-10-10 11:00:44] * Alignment of reads to genome (HISAT2) ./rnaseq_pipeline.sh: line 92: ./hisat2//chrX_data/samples/ERR188044_chrX.alnstats: No such file or directory
I am unable to resolve why there is
// coming up in the last line.