Closed:shell question: How to run multiple paired end alignment in shell?

Question

[John]

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