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?