How to identify adapters in FASTQ file?

Question

[PK]

Dear all, I have seen many answers regarding my doubt. But still, i am not clear. I have some fastq files i did fastqc for quality check. I got overrepresented sequences like this

**SequenceCount       Percentage                     Possible Source**

CTTCACTTCACAACATCTTCTCAACCTTCCAACTCACCTTCCAAACCAC   54899   0.23423784209854648 No Hit
CTCCTTCCTCATCATCAACGCTGCCAACTGCGTTGCCTAAGTGTTTACG   27060   0.11545703942124022 No Hit
CGTCGATGGAGCAGGTGTTGGGGCCGATGGTGGTGGCGCGGGGAACAAC   23766   0.10140251289302274 No Hit

But the problem is in Possible source i did not get any information. please explain to me what I have and how do i process

[dario.garvan]

You shouldn't be guessing the adapters. If the biologists who did the experiment are any good at their job, they will tell you the kit used and the adapter sequences.

[PK]

Okay. But in some fastqc files i found like that.

Answer 1

[shenwei356]

Why not blast them? Blast results show that CTTCACTTCACAACATCTTCTCAACCTTCCAACTCACCTTCCAAACCAC is part of "Neurospora crassa OR74A rodlet protein (eas), mRNA"

[PK]

Thanks for your reply. I have a question here. CTTCACTTCACAACATCTTCTCAACCTTCCAACTCACCTTCCAAACCAC sequences are part of the N.crassa. not an adapters right. but why these sequences comes under overrepresented sequences. In overrepresented sequences describing contamination and adapters sequences.

[shenwei356]

Maybe fastqc judge contamination according to the relative proportion. Adapters? I don't know why.

It also depend on your sample. You didn't say whether N.crassa is part of the sample or not.

[PK]

sorry. I forget to mention. these are the Neurospora crassa samples.

[shenwei356]

So forget the fastqc report and continue downstream analysis. It may be high expressed gene if it's cDNA sequencing sample.

[PK]

Thanks for your answer.