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Old 12-07-2011, 12:56 AM   #1
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Location: Barcelona

Join Date: Nov 2011
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Default How to fix Illumina FASTQ files with read length varies errors

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
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