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  • solexa output files | s_*_seq.txt vs. s_*_sequencece.txt

    Hi All,

    Quick question...

    Why would I be seeing more reads in the s_*_seq.txt files in the Bustard directory that I see in the s_*_sequence.txt files in the Gerald directory (fastq).

    i.e.
    wc -l s_*_seq.txt (normal read file)
    8301558 total

    wc -l s_*_sequence.txt (fastq)
    25885740 s_8_2_sequence.txt

    There should be 4 lines for each read in the fastq files but I am not seeing these numbers line up. Anyone know anything about this?
    Are some sequences excluded from the fastq files compared to the normal sequence files?

    Thanks!

  • #2
    The *_seq.txt files in the Bustard directory include the sequence of every cluster (read). The *_sequences.txt files in the GERALD directory only include the passed filter reads.

    Comment


    • #3
      Ah ok!
      That makes perfect sense then.

      Appreciate the explanation.

      bryan

      Comment


      • #4
        Originally posted by lajoieb View Post
        wc -l s_*_sequence.txt (fastq)
        To count the number of reads in a FASTQ file, you can use grep in -c (counting) mode:

        Code:
        grep -c '^\+' *_sequence.txt
        
        s_6_sequence.txt:4525658
        s_7_sequence.txt:4485601
        s_8_sequence.txt:4099309
        Note you can't match on '@' as that is a valid quality value (Q=0), wherease '+' is not used in Illumina FASTQ. This is easier than dividing by four in your head... although the shell can help us there too:

        Code:
        echo $[ `wc -l < s_6_sequence.txt` / 4 ]
        
        4525658
        Enjoy

        Comment

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