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Old 12-07-2011, 12:56 AM   #1
antgomo
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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
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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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Old 12-07-2011, 01:37 AM   #2
TonyBrooks
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Quote:
Originally Posted by antgomo View Post
How to fix FASTQ files with read length varies errors
0


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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Old 12-07-2011, 05:59 AM   #3
Bukowski
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Submit the original files? I assume yours have already been post-processed/quality trimmed - or they wouldn't be different read lengths in the first place.
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Old 12-08-2011, 01:21 AM   #4
Bukowski
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I notice you got much the same responses over on BioStar: http://biostar.stackexchange.com/que...-varies-errors
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Old 08-19-2014, 03:46 PM   #5
Mamta
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HI all,

Something similar but not exactly the same.
I am having issues with Illumina trueseq custom amplicon data. First Fastqc shows 93% duplication level. Is that a big concern. I have small portion of the genome sequenced
2. There is around 1.3% of unmapped overrepresented reads..Are these adapters. Iam nt sure if its a good idea to trim them.

Lastly I have several regions with only Forward reads and no reverse reads at all... What could be the possible reasons for this?

I would really appreciate if someone could help or direct me to any document/paper that might help.

Thanks a lot!
'Mamta
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Old 08-19-2014, 11:28 PM   #6
dpryan
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@Mamta: Could you post this as a new question? The thread you're posting in hasn't been used in 3 years.
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