Trimming Illumina TrueSeq adapters

Question

[chudar.chudar]

Hi,

I have Controls and treated samples from RNASeq. When I loaded the fastq files onto FastQC, for most of the samples, it didn't showed any IlluminaTrueSeq adapters in over represented sequences but for some samples there were one or two TrueSeq adapter with .1 percentage.

So Should I have to remove these adapters or Can I leave it as it has only .1 percentage of over represented sequences.

Kindly guide me

Regards
Chudar

Answer 1

[michael.ante]

Hi Chudar,

If your read-qualities are a bit sub-optimal, I would go for adapter- and low quality tail trimming using bbduk.

Otherwise, you can map your libraries (e.g two adapter-contaminated and two adapter-free ones) and compare the mapping statistics.

I would guess that there'll be only negligible differences with 0.1% adapter contamination.

Cheers,
Michael