Creating a script to run STAR alignment on multiple fastq files

Question

[mropri]

I have fastq files named in the following way:

rep1_A01_R2.fastq rep1_A02_R2.fastq rep1_B01_R2.fastq rep1_B02_R2.fastq rep1_C01_R2.fastq rep1_C02_R2.fastq rep1_D01_R2.fastq rep1_D02_R2.fastq

and many more with the same convention of letters and numbers.

I know how to run STAR, was just wondering if there is a way so when I read in the files I do not have to list all the files but can create a command that pulls each fastq file and runs alignment on it. Appreciate any help.

Answer 1

[Pierre Lindenbaum]

https://raw.githubusercontent.com/alexdobin/STAR/d14a0a992f94ba3a64c26dd08ac58e2b4ab134f3/doc/STARmanual.pdf

Multiple samples can be mapped in one run with a single output. This is equivalent to concatenating the read files before mapping, except that distinct read groups can be used in --outSAMattrRGline command to keep track of reads from different files. For single-end reads use a comma separated list (no spaces around commas), e.g.: --readFilesIn sample1.fq,sample2.fq,sample3.fq

For paired-end reads, use comma separated list for read1, followed by space, followed by comma separated list for read2, e.g.: --readFilesIn s1read1.fq,s2read1.fq,s3read1.fq s1read2.fq,s2read2.fq,s3read2.fq

[ATpoint]

I think OP is looking for a simple loop rather than pooling everything into a single run or doing RG magic.

[mropri]

that would be helpful as well. If you have something in mind. I tried creating a for loop with sed but am getting stuck.

[mropri]

Thank you!