For loop rna sequencing alignment

Question

[kcarey]

Hey guys... I am trying to do a for loop to align my samples to a reference file in terminal.....can someone help me...I am getting this error:

EXITING because of fatal input ERROR: could not open readFilesIn=Read1

This is the code I put in

for f1 in `cat MatchedFastqList.txt` ;do SAMPLE=$(echo ${f1}| sed "s/_1\.fastq\//"); echo ${SAMPLE}.bam; echo 
STAR --runThreadN 16 --genomeDir /folder/to/project/ncbi-genomes-2022-09-19/
GCF_000001405.40_GRCh38.p14_genomic.fna --sjdbGTFfile /folder/to/projects/GCF_000001405.40_GRCh38.p14_genomic.gtf 
--readFilesIn ${f1} --outReadsUnmapped Fastx ; done

[Pierre Lindenbaum]

not an answer but : you'd better use a workflow manager like snakemake or nextflow.

..I am getting this error

what is "this error" ?

[kcarey]

Thank you for your feedback. I am self-taught learning coding. What is a workflow manager? Is it super beneficial for longer pipelines?

[Pierre Lindenbaum]

Is it super beneficial for longer pipelines?

definitively

https://pubmed.ncbi.nlm.nih.gov/28398311/

Nextflow enables reproducible computational workflows

https://pubmed.ncbi.nlm.nih.gov/35037206/

Pipeline Automation via Snakemake

[iraun]

404: Error Not Found

(Now seriously, you forgot to copy the error ;) )

So far the only thing that I can see is that the done in the end of the loop is missing.

[kcarey]

Sorry, I was rushing I got this error

EXITING because of fatal input ERROR: could not open readFilesIn=Read1

It also is not going down the list to each file...

[iraun]

Can you copy-paste the content of MatchedFastqList.txt?

[kcarey]

It contacts samples that are set up like this "Sample345.fastq" and its all listed