How To Fix Fastq Files With Read Length Varies Errors

Question

[Tonig]

Dear List,

I am a newbie in NGS analysis, I've got a collection of FASTQ files coming from a NGS analysis, I tried to upload in GEO and I had this reply from the curator:

These fastq files have "read length varies" errors All reads in a fastq file should be the same length. Read lengths of different size originating from a single lane is an error

So, is there any solution to deal with this? I mean, do I have to trim the fastq's or anything similar? I guess that prior to this I have to use FASTQC in order to see what are the length variations? Do you have any idea?

Thanks in advance

[Neilfws]

Contacting the facility and asking for the raw data is the solution to fix it. You can't put back what's been removed when you don't know what was done.

[Alastair Kerr]

If the read lengths vary, it sounds like they have been trimmed already. I believe the curator is looking for the original data.

[Tonig]

OK, thanks, maybe that's the problem i'll try to contactthe guys from the facility, however, is there any solution to fixt it?

[Damian Kao]

what NGS platform is it?

[Tonig]

Illumina, thanks everybody, I mailed th facility and look fro a reply

[Tonig]

I contacted the facility, and I am waiting for a reply, I agree that all the problem rely on FASTQ original data. The platform is Illumina, we are working with Methylomes and They sent us "clean data", probably trimmed. Thanks everybody for the fast replies