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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
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  • $\begingroup$ I only see two GSM IDs in your output, is it the extra SRR* files you don't want? I don't really have much experience with the SRA, but I can see that, for example, SRR12180300 is under GSM4663476: ncbi.nlm.nih.gov/sra/?term=SRR12180300. Are you sure there is an issue here? $\endgroup$
    – terdon
    Aug 8, 2023 at 10:51
  • $\begingroup$ yes I mean if two GSM ID then 2 SRR file I should be getting but which is SRR12180300 and SRR14836042 for the other GSM ID but Im getting other also why? $\endgroup$
    – PesKchan
    Aug 8, 2023 at 14:30
  • $\begingroup$ @terdon these are technical reads which I don't want in other words i need final output where I get only one output instead of different technical reads i thought fasterq-dump would do this by default but it it not doing it $\endgroup$
    – PesKchan
    Aug 8, 2023 at 18:16

1 Answer 1

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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
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  • $\begingroup$ "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". it is okay to go head with this approach meaning it wont be an issue with the downstream alignment .? $\endgroup$
    – PesKchan
    Aug 9, 2023 at 19:08
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    $\begingroup$ cat is fine, see edit. $\endgroup$
    – ATpoint
    Aug 10, 2023 at 11:31

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