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  • Concatenate several SRA reads to a single fastq file

    Hi all,

    I want to re-analyse a dataset available in GEO:

    I've downloaded all the files, however it seems that each replicate/experiment has several file corresponding to several runs. The question is: how to concatenate these runs once they are converted into fastq? Would a simple cat command work?

    Also, is this a silly thing to do? (I'm a newbie) Ultimately my goal is to determine gene expression changes.

    Cheers.

  • #2
    [QUOTE=krespim;80152]

    I've downloaded all the files, however it seems that each replicate/experiment has several file corresponding to several runs. The question is: how to concatenate these runs once they are converted into fastq? Would a simple cat command work?
    [./QUOTE]

    I'm sorry, why exactly do you want to cat all these files? A simple a simple
    cat *.fastq >> consolidated_fastq.fq

    will be fine but whats your need for doing so? Every single run usually corresponds to a different sample so why merge all?

    Originally posted by krespim View Post

    Also, is this a silly thing to do? (I'm a newbie) Ultimately my goal is to determine gene expression changes.

    Cheers.
    Process files separately then use comparitive studies on the sam/bam files!

    Comment


    • #3
      Originally posted by arkal View Post
      will be fine but whats your need for doing so? Every single run usually corresponds to a different sample so why merge all?
      Well, this is actually my main issue as I don't know if each run is a different sample, or the same sample ran in multiple lanes. The sample GEO page lists 3 SRA files.

      The paper does not mention biological or technical replicates.

      Comment


      • #4
        Originally posted by krespim View Post
        Well, this is actually my main issue as I don't know if each run is a different sample, or the same sample ran in multiple lanes. The sample GEO page lists 3 SRA files.

        The paper does not mention biological or technical replicates.
        It seems to be the same sample in different lanes/runs... so you can either merge the fastqs and align or align the 3 separately and merge the sams! I recommend the latter as it will take less time (provide you have the resources to align them parallelly)!

        Comment


        • #5
          Originally posted by arkal View Post
          It seems to be the same sample in different lanes/runs... so you can either merge the fastqs and align or align the 3 separately and merge the sams! I recommend the latter as it will take less time (provide you have the resources to align them parallelly)!
          I have recently been granted access to a server with a very decent number or processors so that should be easy

          Thanks a lot arkal!

          Comment


          • #6
            No worries all the best!

            Comment

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