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Old 04-22-2020, 12:04 PM   #1
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Location: Boston, MA, USA

Join Date: Apr 2020
Posts: 5
Default Poor seq quality due to low diversity sample


I have some sets of HiSeq data that I am analyzing and the sequencing quality turned out quite bad. I attach the "per base seq quality" diagram and the "per tile seq quality" diagram for one of those sets, generated using FastQC.

I contacted the service provider, and they say it's due to my sample having low diversity especially at the beginning. (I also attached the seq content diagram.)
Based on some searches and reading of Illumina tech notes, I see that the diversity at the first several bases is quite important for the system to "calibrate" correctly for quality base calls for later bases.
My first question is, is this roughly a correct interpretation? And is there any way to "post-process" maybe the raw(er) data to correct/improve the seq reads?

Second, what I still don't understand is why does it affect the per tile seq quality? How does the low diversity at initial bases have anything to do with the spatial variation on seq quality?

What do you guys think?
What should I argue when replying to my service provider? Should I ask for a re-run?

Any note will be greatly appreciated!
Attached Images
File Type: png Per_base_seq_quality-SW3-R1.png (12.3 KB, 10 views)
File Type: png Per_tile_seq_quality-SW3-R1.png (12.1 KB, 7 views)
File Type: png Per_base_seq_content-SW3-R1.png (110.5 KB, 12 views)

Last edited by invu; 04-22-2020 at 12:06 PM.
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