Question: This File Contains Inconsistent Headers
gravatar for gtasource
11 weeks ago by
gtasource30 wrote:

Illumnia Base Space is giving me this error that my FASTQ files have inconsistent header information.

This file contains inconsistent header information. We expected all cluster headers to match '@Sample:116:FlowId:1:1101:19361:1047:N:0:AGTCAACA+TCTTTCCC#0/1' but we encountered the header '@Sample:116:FlowID:1:1101:23023:1063**:N:0:AGTCAACA+TCTTTCCC#0/1' at cluster 2.

I edited parts of the header sample names, but as you can see, the header differs at this position: 19361:1047 23023:1063

Are there any tools I can use to fix this header issue?


ADD COMMENTlink modified 11 weeks ago by swbarnes27.0k • written 11 weeks ago by gtasource30

I think the part that is causing problems may be the asterisks [*] rather than what you indicated. It is normal that headers have different numbering, but asterisks are what to my eye is inconsistent.

ADD REPLYlink written 11 weeks ago by Mensur Dlakic2.5k

The last two numbers in the read name are xy coordinates on the flow cell tile...they absolutely are supposed to be different for every read.

ADD REPLYlink written 11 weeks ago by swbarnes27.0k
gravatar for swbarnes2
11 weeks ago by
United States
swbarnes27.0k wrote:

a sed command would probably fix things, but I'd worry where there's one error, there might be more. Where did you get this fastq? How was it generated?

ADD COMMENTlink written 11 weeks ago by swbarnes27.0k

The FASTQ file that is giving the errors was generated from Kneaddata to remove human data from the dataset (we are doing a metagenomics analysis.) When uploading the original FASTQ file, no header issues are given.

I don't have to use Kneaddata for removal of the human contamination using a reference genome. But it seemed easier than using an aligner, removing the unmapped BAM and converting to a FASTQ file (I also feel like this would give FASTQ issues as well.)

ADD REPLYlink written 11 weeks ago by gtasource30
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