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Forum: Illumina/Solexa 04-23-2020, 09:30 AM
Replies: 9
Views: 1,907
Posted By invu
I see. Next time I will consider PhiX spike-in....

I see. Next time I will consider PhiX spike-in. Thanks, cement_head!
Forum: Illumina/Solexa 04-23-2020, 05:33 AM
Replies: 9
Views: 1,907
Posted By invu
Thanks, ATϟGC, that's a good suggestion. ...

Thanks, ATϟGC, that's a good suggestion.
Looking back, the adapter-primers that I had used for my older runs when I didn't have this issue, did have some degenerate bases in between for different...
Forum: Illumina/Solexa 04-22-2020, 06:20 PM
Replies: 9
Views: 1,907
Posted By invu
Ha, I see. Lesson learned. Thanks for your help,...

Ha, I see. Lesson learned. Thanks for your help, GenoMax!
Forum: Illumina/Solexa 04-22-2020, 02:29 PM
Replies: 9
Views: 1,907
Posted By invu
Thanks for your reply, GenoMax! The sample is a...

Thanks for your reply, GenoMax!
The sample is a custom set of sequences with well-defined regions (hence those low-diversity regions). I had declined PhiX spike-in to obtain as many valid read lines...
Forum: Illumina/Solexa 04-22-2020, 11:04 AM
Replies: 9
Views: 1,907
Posted By invu
Poor seq quality due to low diversity sample

Hi,

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...
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