Question: Thoughts on a few bad tiles per sequencing run
1
gravatar for Biogeek
2.7 years ago by
Biogeek350
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?

Thanks.

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

sequencing tiles • 1.2k views
ADD COMMENTlink modified 2.7 years ago by Devon Ryan89k • written 2.7 years ago by Biogeek350
1

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
1
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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