Multiple SRR ID downloaded for single GSM IDs input issue

Question

So here I'm trying to donwload multiple fastq files based on the GSM ID input the script works fine when then input is only SRR id but it runs into error when it is given GSM ID

My small GSM ID input set

cat srr_id.txt
GSM5369701
GSM4663476

Answer 1

Basically you're asking why a given GEO accession (GSM...) has many Runs (SRR...). That is because the submitters uploaded multiple fastq files for the same sample, which is the case if a library has been sequenced over multiple lanes or flowcells, often to increase depth. You can use cat to combine these "technical replicates" into a single fastq file for both R1 and R2 file in case of paired-end data, or one single fastq file in case of single-end data.

For example, if you have file1.fq.gz, file2.fq.gz and file3.fq.gz just do:

cat file1.fq.gz file2.fq.gz file3.fq.gz > combined.fq.gz