Entering edit mode
5.0 years ago
John
▴
270
Hi there,
the following command works with bash(Mac command line), but not with unix shell(after entering screen
command), how do I rewrite it?
for i in $(ls ~/mbd1rnaseq/scfastq | rev | cut -c 9- | rev | uniq)
do rsem-calculate-expression -p 8 --forward-prob 0.95 --bowtie2 --bowtie2-path /mnt/software/bowtie2/default --output-genome-bam --paired-end ~/mbd1rnaseq/scfastq/${i}R1.fastq ~/mbd1rnaseq/scfastq/${i}R2.fastq ~/mbd1rnaseq/mm9.rsem ${i}
done |& tee terminaloutput.txt
Basically , file input names got changed.
Error: Must specify at least one read input with -U/-1/-2 (ERR): bowtie2-align exited with value 1 sh: 32m05_CGTACTAG-GCGTAAGA_R2.fR1.fastq: command not found sh: 32m05_CGTACTAG-GCGTAAGA_R2.fR2.fastq: command not found sh: 32m05_CGTACTAG-GCGTAAGA_R2.f.temp/o such file or directo
my file names are like this:
11_AGGCAGAA-TATCCTCT_R1.fastq 39_CGTACTAG-ACTGCATA_R1.fastq 60_GGACTCCT-TATCCTCT_R1.fastq 77_CTCTCTAC-AGAGTAGA_R1.fastq
11_AGGCAGAA-TATCCTCT_R2.fastq 39_CGTACTAG-ACTGCATA_R2.fastq 60_GGACTCCT-TATCCTCT_R2.fastq 77_CTCTCTAC-AGAGTAGA_R2.fastq