Question: Thoughts on a few bad tiles per sequencing run
gravatar for Biogeek
2.7 years ago by
Biogeek350 wrote:

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?


sequencing tiles • 1.2k views
ADD COMMENTlink modified 2.7 years ago by Devon Ryan89k • written 2.7 years ago by Biogeek350

Just follow your standard protocol. A couple of bad tiles are not going to cause major issues.

ADD REPLYlink written 2.7 years ago by genomax65k
gravatar for Devon Ryan
2.7 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

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

ADD COMMENTlink written 2.7 years ago by Devon Ryan89k
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