Question: Quality check of Medip Seq Data
0
gravatar for gskbioinfo143
2.7 years ago by
India
gskbioinfo14350 wrote:

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

ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 2.7 years ago by gskbioinfo14350

You didn't find any overrepresented sequences?

ADD REPLYlink written 2.7 years ago by Satyajeet Khare1.4k

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.

ADD REPLYlink written 2.7 years ago by gskbioinfo14350

Is this NextSeq or MiniSeq data?

ADD REPLYlink written 2.7 years ago by WouterDeCoster40k

yes its from NextSeq

ADD REPLYlink written 2.7 years ago by gskbioinfo14350
1

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

ADD REPLYlink written 2.7 years ago by WouterDeCoster40k

what about the Kmer content?

ADD REPLYlink written 2.7 years ago by gskbioinfo14350
0
gravatar for mks002
2.7 years ago by
mks002170
Bangalore. India
mks002170 wrote:

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.

ADD COMMENTlink written 2.7 years ago by mks002170
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