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Old 12-07-2011, 01:37 AM   #2
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Originally Posted by antgomo View Post
How to fix FASTQ files with read length varies errors

Dear List,

I am a newbie in NGS analysis, I've got a collection of FASTQ files coming from an Illumina 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
You shouldn't be getting different readlengths off an Illumina sequencer.
If the file was downloaded, I'd check the md5sums to make sure the file is intact and not corrupted during download.
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