Confusion Regarding Tape Station Peak

Question

[Bhavya]

Hi

I made a transcriptome library. I ran a tape station on it. Expected size of the library was ~300 bp. My peak came around 293 bp. Though the peak height was not very good, it was visible.

It is showing another line indicating peak size around 49 bp, but there is no visible peak at all, only just a line.

When I checked the percentage of integrated peak area 77.96 is coming for just this line, whereas for my peak (which is though low in height, but very much visible) it is 22.04.

Has anyone faced this type of issue? I am eagerly waiting for your comments.

Bhabhya

[Carlo Yague]

Could it be adapter or primer contamination ? Does it look like something like this ?

Primer/adapter contamination might indicate issues in library preparation, including insufficient library clean-up on magnetic beads. Repeating the last clean-up of the library prep protocol might solve the issue (small fragments are excluded in those clean-ups).

[colindaven]

This is a bioinformatics forum and this question is a wet lab question. You might get more responses on seqanswers.com.