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How to tell if a FastQ file is a concatinate of 2 seperate illumina runs?
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17 months ago
landrjos • 10

Hi All,

I have a fastQ file which was left by a student which I suspect is a file which is a concatenate of a HiSeq run and a smaller MiSeq run. How do I determine if this is the case? The distribution of read length is uniform at 101 bp.

sequence • 839 views
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Were the headers edited or that student has retained the original ones?

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Can you run "head my.fastq" and "tail my.fastq" on your file and paste the results here? One should be able to make a fair guess based on that.

Strictly speaking however, it's not possible to be able to determine this in all situations. FASTQ is a terrible file format for metadata.

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FASTQ is a terrible file format

Fixed that for you.

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Hahah, hey man :)

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10 weeks ago
genomax 68k
United States

Since you are referring to there being data from two different sequencer types the following should work. There are unique barcodes on flowcells from different types of sequencers. Following also assumes that fastq headers have not been modified in any way.

Out the following code in a file (barcode.awk) :

BEGIN { FS = ":"; }

((NR % 4) == 1) { barcodes[$3]++; }

END {
  for (bc in barcodes) {
            print bc": "barcodes[bc]"";
    }
}

then run like this: zcat your.fastq.gz | awk -f barcode.awk. It should tell you if you have one or more barcodes represented along with the number of reads for each type. If your data is not compressed then cat your.fastq | awk -f barcode.awk should be used.

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Thanks a lot,

This script is reporting the flow cell for the runs. Is there a modification that could be made to report what the barcode or index sequence is?

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If you replace $3 above with $10 it will report index sequences. You can't make out if you have data from multiple sequencers from this information unless you have some prior information about the contents of the pools.

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I think with both the flow cell and barcode information from the fast q files I can figure it out. Thanks for your help.

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