Fishy HiSeq2000 reads length

Question

[Lim]

Dear community,

Good day.

I received a set of paired-end HiSeq2000 reads (Illumina 1.9) which was generated in 2012 from my colleague . The length of reads is 150 bases in both directions.

The reads contain TruSeq adapter sequences, thus, I trimmed them with cutadapt tool. After that, I checked the reads with FastQC. The adapter sequences were successfully trimmed according to FastQC report.

Question is, many reads still in 150 bases long. These reads seem fishy to me. Does anyone has this experience before?

Thank you for your time.

Best regards,
KJ Lim

Answer 1

[Ido Tamir]

What seems fishy? The read length? While there is no official 150bp PE run on the HiSeq 2000, I know of labs that did it in 2012 or 2013. So unless you see a very strong quality drop or strange artifacts in the reads towards the end there is no reason to automatically declare them bad just because of the read length.

[Lim]

Ido Tamir, the read length seems fishy and as you said there is no official 150 bases HiSeq sequencing.
I maybe wrong on this, thus, I would to learn from community experiences. Thanks for your replied.

[Brian Bushnell]

We sequence 150bp on HiSeq almost exclusively, and were doing so in 2012.

[Lim]

Brian Bushnell thanks for sharing your experience.

Answer 2

[Devon Ryan]

There's nothing particularly fishy here. You don't expect to see adapter contamination in all of your reads, at least unless you were doing small RNAseq...but then you wouldn't use 150bp PE reads to begin with. Typically only a single-digit percent of reads will show adapter contamination in normal RNAseq datasets, so it's common to have most reads remain untrimmed.

[Lim]

Thanks for your reply, Devon Ryan.