ENCODE RNA-seq Quality

[Dario1984]

Has anyone worked with ENCODE data much ? I'm just starting to visualise it, and there's some strange mappings going on. So many mismatches.

I downloaded the BAM file. I did not do this mapping myself.

The accession is wgEncodeEH000135. It's 75 base pair single end RNA-seq data of HepG2.

[droog_22]

Update IGV

Hi,

I once had many mismatches in another dataset which I aligned with novoalign. It was only later that I found out that novoalign introduces soft-clipped bases which my installed version of IGV could not display properly. I could easily fix this by installing the latest version of the software.

You can give it a try, maybe the mismatches you see in IGV are just a visualisation problem.

Cheers

[davisc]

I would point you to more recent ENCODE RNA-Seq data. There were issues in the "beginning" with Illumina sequencing reagents leading to high error rates. That dataset may have been from that time. It's gotten much, much better.

http://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?hgsid=2641755&c=chr17&g=wgEncodeCshlLongRnaSeq