Help with for loop for sequence alignment using STAR

Question

[Amaranta Remedios]

Hi, I am trying to run a sequence alignment with STAR. I have a total of 28 files paired-end files, 14 R1 and 14 R2. My files are called like this:

mapped_trimmed.LLC7b_Aligned.sortedByCoord.out.bam_R2.fq
mapped_trimmed.LLC7a_Aligned.sortedByCoord.out.bam_R2.fq
mapped_trimmed.LLC1b_Aligned.sortedByCoord.out.bam_R2.fq
mapped_trimmed.LLC1a_Aligned.sortedByCoord.out.bam_R2.fq
mapped_trimmed.LLC7b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC7a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC1b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC1a_Aligned.sortedByCoord.out.bam_R1.fqq

The code I have written to run star so far is this one:

#!/bin/bash --login
#$ -cwd
#$ -l short
#$ -pe smp.pe 12

module load apps/intel-18.0/star/2.7.2b

#get only files names
for i in *R1.fq; do name=$(basename ${i} _R1.fq);

  STAR --genomeDir /scratch/STAR_index  \ #Path to the index generated previously
   --runThreadN 12 \ #Number of cores
   --readFilesIn ${name}_R1.fq ${name}_R2.fq \ #Path to the input files (forward and reverse)
  --outFileNamePrefix ${name}_aligned_transcriptome \ #Prefix to the output files
  --outSAMtype BAM SortedByCoordinate \ 
  --limitBAMsortRAM 31000000000
done

Yet I keep getting this error

/opt/site/sge/default/spool/node403/job_scripts/1635775: line 17: syntax error near unexpected token `('
/opt/site/sge/default/spool/node403/job_scripts/1635775: line 17: `  --readFilesIn ${name}_R1.fq ${name}_R2.fq \ #Path to the input files (forward and reverse)'`

This is the output of the part of the code that should feed into line 17

for i in *R1.fq; do name=$(basename ${i} _R1.fq); echo $name
> done 
mapped_trimmed.LLC1a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC1b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC2a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC2b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC3a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC3b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC4a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC4b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC5a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC5b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC6a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC6b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC7a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC7b_Aligned.sortedByCoord.out.bam

And this is line 17 itself and it looks alright. So, I don't understand why this loop is not working

for i in *R1.fq; do name=$(basename ${i} _R1.fq); echo ${name}_R1.fq; done
mapped_trimmed.LLC1a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC1b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC2a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC2b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC3a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC3b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC4a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC4b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC5a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC5b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC6a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC6b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC7a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC7b_Aligned.sortedByCoord.out.bam_R1.fq

Which is exactly how the files are called in my folder.

I hope someone can help me!

[rpolicastro]

You seem to be pointing to a salmon transcriptome index instead of a STAR genome index.

[Amaranta Remedios]

I corrected that, I can see how that would be confusing. Thanks, It really is a STAR index

[Pierre Lindenbaum]

for i in *R1.fq; do name=$(basename ${i} _R1.fq);

use a workflow manager like nextflow or snakemake

[Pierre Lindenbaum]

anscripts/Genome \ #Path to the index genera

I'm not sure bash likes the strings after a \

Answer 1

[Pierre Lindenbaum]

e \ #Path to the index generated previously

remove any string after a \ , even if it's a space or a comment....