What are your percentages? Proportion of reads containing at least one adapter? Proportion of total bases matching adapters?
How are you counting the grep matches? One per line (i.e. one per sequence), or might it count multiple matches per line?
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FastQC; overrepresented sequences versus a grep
Hi,
I have an odd observation with fastQC's figure for over-represented sequences versus the number I get out when I do a simple egrep for adapter sequences in the .fastq file.
FastQC tells me I have adapter contamination. And how much. Excellent tool!
When I take this info and do a simple egrep for the Universal adapter sequence & for the library-appropriate indexed TruSeq adapter sequence I get waaaaaaay more 'hits' than FastQC reports
for example, FastQC says 5.31% adapter
egrep says 21%
There must be a simple explanation?! Suggestions welcome.
M
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