Quality check of Medip Seq Data

Question

[gskbioinfo143]

Dear sir/mam,

Hi

i have query regarding Quality check analysis using fastqc. please need help i have done QC analysis for MEDIP SEQ data from illumina using fastqc following parameters didn't pass the criteria(images attached).

1. Per base sequence content
2. Per sequence GC content
3. Sequence Length Distribution
4. Sequence Duplication Levels
5. Overrepresented sequences
6. Kmer Content

https://postimg.org/gallery/1eoe8a78g/

the rest parameters passed the criteria. is it fine to go ahead with alignment or shall i trim the sequence length.

Thank you

[Satyajeet Khare]

You didn't find any overrepresented sequences?

[gskbioinfo143]

yes in one of the fastq file it had overrepresented sequence of GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

other fastq file is good.

i have trim the data using Trimmomatic and Trim Galore tool (defaults settings) in galaxy and did fastqc but still QC images shows the same.

please need help.

[WouterDeCoster]

Is this NextSeq or MiniSeq data?

[gskbioinfo143]

yes its from NextSeq

[WouterDeCoster]

That explains polyG stretches, due to the two-colour chemistry. G means absence of signal. Probably best to trim polyG tails. For more information, see this post on qcfail

[gskbioinfo143]

what about the Kmer content?

Answer 1

[mks002]

You can do a simple check for per base quality result from FastQC. If there is quality drop, you can do trimming based on quality and then check the fastQC of the trimmed data.