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Old 08-13-2013, 10:26 AM   #1
mattanswers
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Default fastqc kmer relative enrichment

I was wondering how to interpret the Kmer content graph in fastqc. I have attached it. It seems from my graph that 50% of all reads have the 6 kmers listed ? Is this a normal graph ?
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Last edited by mattanswers; 08-13-2013 at 10:29 AM. Reason: need to attach .png file
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Old 08-13-2013, 11:55 AM   #2
GenoMax
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Is this RNA-seq data?

Following thread may be useful (though it refers to a MiSeq run the issue is applicable to illumina sequencing in general): http://seqanswers.com/forums/showthread.php?t=30448

One more: http://seqanswers.com/forums/showthread.php?t=17219

Last edited by GenoMax; 08-13-2013 at 11:57 AM.
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Old 08-13-2013, 12:18 PM   #3
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Thank you very much, GenoMax, for the links. They are very informative.

This is RNA-Seq. It seems the first 12 or so bases are due to 'random' priming, but I was also wondering about why the lines on the graph stay up at ~50% for the length of the graph ? Random priming would explain the first 12 or so bases, but why the steady % for the rest of the sequence ?
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Old 08-13-2013, 02:48 PM   #4
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Quote:
Originally Posted by mattanswers View Post
Thank you very much, GenoMax, for the links. They are very informative.

This is RNA-Seq. It seems the first 12 or so bases are due to 'random' priming, but I was also wondering about why the lines on the graph stay up at ~50% for the length of the graph ? Random priming would explain the first 12 or so bases, but why the steady % for the rest of the sequence ?
http://www.bioinformatics.babraham.a...d%20Kmers.html
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Old 08-14-2013, 11:20 AM   #5
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Thanks again for your help, GenoMax.

My sequence length is only 50 bases and the quality is very good.

From what I read on the linked site, it seems that I have 6 kmers that are 50-fold enriched throughout the length of my sequence. But what does this mean in terms of sample quality ?

If I have 25-30 million reads and there is a 50 fold enrichment of these kmers (most likely I would guess from the adaptor) then how many sequences does that affect ? So, if there were 100,000 sequences in which had adaptor sequence at various positions other than the end of the sequence what would the fold-enrichment be ? 100,000 affected sequences may be enough to make the fold-enrichment high, but they are only a small percentage of the total. On the other hand, if I had a much smaller number of total sequences, then the fold-enrichment may be a problem. So, I guess I want to know how to relate fold-enrichment and total number of sequences in order to tell if the fold-enrichment is a problem or just from an insignificant part of the total.
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