Thoughts on a few bad tiles per sequencing run
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4.8 years ago
Biogeek ▴ 400

I was doing some reading and came across the Macmanes article discussing how minimal trimming is better than stringent trimming for mapability in RNA-Seq reads.

For Trimmomatic I used such settings:

'adapters/TruSeq3-PE-2.fa:2:30:10 HEADCROP:13 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:5 MINLEN:25'

Whilst my sequence per bp quality is high, and my per base sequence content also. My per tile quality was flagged red due to 2 bad tiles (image link below). What would one do, I've seen flow cells with major tile problems across the whole cell. Do 2 cells make a big impact on the data, is there anyway to remove these, or would one bother given the other test parameters passed?

Additionally my kmer content is flagged;however I've read this is typical and not a problem?

Thanks.

https://postimg.org/image/fbtwek7wl/

tiles sequencing • 1.7k views
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Just follow your standard protocol. A couple of bad tiles are not going to cause major issues.

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4.8 years ago

Don't worry about a couple bade tiles. The fastQC kmer thing always fails in RNAseq, ignore it.

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