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Old 12-03-2010, 06:41 AM   #1
frymor
Senior Member
 
Location: Germany

Join Date: May 2010
Posts: 149
Unhappy Fastqc results small RNA run

Hi,

I got a data set of small RNAs. They did polysome profiling followed by sequencing of the regions covered by the ribosomes.

Unfortunately the results from Fastqc are not as expected.
The problem is, I am not exactly sure how to interpret the data and what to say about the quality of it either than good/bad.

I am happy to get any advices as to what went wrong or what ca be done better.

Is it a problem of the library creation, the method of preparation or else?

I added here the images I found very disturbing.

per_base_sequence_content.jpg

per_base_gc_content.jpg

per_sequence_gc_content.jpg

The total quality of the sequences is quite good as you can see from the per_base_quality image.

per_base_quality.jpg

Another problem I have is the overrepresented sequences. I have one read in my library in over 33% of the reads. Than I have some more reads, but with much lower concentration (7% downwards). the kmer content show also a strange behavior.

kmer_profiles.jpg

I will be grateful for any suggestions of improvements or possible explanations for this results.

Thanks for any help

Assa
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