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  • SPAdes: with different read length

    Hi members,

    I'm facing something weird. I know not all reads in the fastq files can have same length.
    But in my trimmed data, read length of reverse and forward files are different. I checked out for only first read, though.

    Data: paired end
    Organism: E. coli

    Output 101 from reverse strand:

    Code:
    zcat sample_R2_trimmed.fastq.gz | awk '{if(NR%4==2) print length($1)}'  | head -1
    Output 54 from forward strand:

    Code:
    zcat sample_R1_trimmed.fastq.gz | awk '{if(NR%4==2) print length($1)}'  | head -1
    An icing to this dilemma is, SPAdes uses 55 as K-mer during assembly. And the genome size from assembly is reasonable.

    My questions:

    1) Shouldn't SPAdes select K-mer less than 55 here?
    Bioinformaticscally calm

  • #2
    Can you tell us why are they different (and uniformly of length 54 for R1)? Did you trim them that way?

    Comment


    • #3
      Hi Genomax,
      Thanks for your reply.

      I've 2 sets of data, trimmed (sequencing center did this trimming based on the quality)and untrimmed. I used the already trimmed data for assembly.

      Oh, they aren't uniform ( looking at already trimmed file).
      Have 72 different lengths: max is 101, minimum 30.
      So, in a way, all numbers from 30-101 are present for read lengths. That's strange. :-/
      Last edited by bio_informatics; 06-10-2015, 07:50 AM.
      Bioinformaticscally calm

      Comment


      • #4
        In that case your original question is no longer applicable, correct?

        Comment


        • #5
          Yes.
          Sorry.

          Originally posted by GenoMax View Post
          In that case your original question is no longer applicable, correct?
          Bioinformaticscally calm

          Comment


          • #6
            No problem. Sounds like you did get a reasonable sized assembly so all should be well.

            Comment


            • #7
              Yes, that is more important.
              Merci!
              Bioinformaticscally calm

              Comment

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