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Old 08-21-2015, 09:49 AM   #1
wendytezuka
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Location: MI

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Default Help! FastQC problem on drosophila RNA-seq data!

I have app 70 RNA-seq samples on drosophila. When going through the FastQC, there are three red flags to almost all the samples. I'm new to this field and could anyone tell what was wrong and what I should do (please in some details)? Great thanks!
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File Type: png QC_Kmer content.PNG (80.0 KB, 12 views)
File Type: png QC_per base sequence content.PNG (81.3 KB, 10 views)
File Type: png QC_per sequence GC content.PNG (57.8 KB, 10 views)

Last edited by wendytezuka; 08-21-2015 at 09:53 AM.
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Old 08-21-2015, 10:02 AM   #2
GenoMax
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Short answer .. no need to worry. Proceed with data analysis.

http://seqanswers.com/forums/showthread.php?t=17219 and other links within this thread.

A "failed' flag in FastQC should be considered as a guide. It does not automatically mean that the data is bad.

The GC plot "bulge" may represent bacterial (endo-symbionts) that some drosophila populations have. (This may or may not apply in your case).

Last edited by GenoMax; 08-21-2015 at 10:08 AM.
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