STAR Alignment Traces

[dlbuz]

Hello,

I'm sure this is a simple question to answer but I recently started using STAR to align my RNA-seq data and I have a question about the traces it gives.

I uploaded a file that shows a strange shaped peak around 432,000 in 4 biological replicates of RNA-seq I did. I know this is mapped to a specific tRNA sequence but why does the aligner shape it like such that it's a rectangle with a bump on top? This is also true for all tRNA sequences I looked at. Does the STAR alignment have problem with short repetitive sequence lengths?

Also, this is after doing normalization by log10 and then RPM.

Thanks!

[dpryan]

How long is the tRNA and how long are your reads?

[dlbuz]

How long is the tRNA and how long are your reads?

We did 33 nt paired end sequencing on MiSeq platform. The RNA was barcoded using the Illumina Stranded mRNA Library Prep kit. The tRNA sequence are usually 350-400 bp give or take a few bp.

It may not be a STAR issue, but actually a bedtools issue with genomecoveragebed. It's also possible that tRNA RNA-seq data is supposed to look like this.