Question: How to tell if a FastQ file is a concatinate of 2 seperate illumina runs?
0
gravatar for landrjos
21 months ago by
landrjos10
landrjos10 wrote:

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 • 849 views
ADD COMMENTlink modified 21 months ago by genomax70k • written 21 months ago by landrjos10
1

Were the headers edited or that student has retained the original ones?

ADD REPLYlink written 21 months ago by lakhujanivijay4.3k

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.

ADD REPLYlink written 21 months ago by John12k
1

FASTQ is a terrible file format

Fixed that for you.

ADD REPLYlink written 21 months ago by WouterDeCoster40k

Hahah, hey man :)

ADD REPLYlink written 21 months ago by John12k
0
gravatar for genomax
21 months ago by
genomax70k
United States
genomax70k wrote:

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.

ADD COMMENTlink modified 21 months ago • written 21 months ago by genomax70k

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?

ADD REPLYlink written 21 months ago by landrjos10

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.

ADD REPLYlink written 21 months ago by genomax70k

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

ADD REPLYlink written 21 months ago by landrjos10
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