Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
How to use HTSeq to count RNA-Seq overlap w/ whole genes (intron+exon) vs. exon only achamess Bioinformatics 1 02-20-2017 11:36 PM
Extract exon-intron reads from RNA-Seq data aggp11 RNA Sequencing 1 11-26-2014 08:17 AM
Intrasample exon analysis of RNA-Seq data using RPKM values desmo Bioinformatics 0 09-04-2014 02:57 AM

Thread Tools
Old 04-06-2018, 10:47 AM   #1
Junior Member
Location: New Jersey

Join Date: Apr 2011
Posts: 6
Default RNA-seq data not mapping to exon

We did RNA-seq on sperm cells. RNA is more on the degraded size. Because there is no good ribosomal removal kit for this species, we proceeded with KAPA hyper kit which is poly-dT based.
Now, upon mapping data is quite odd, never seen before. Reads are not aligning to the exons, instead, it seems quite random, going virtually anywhere in patches. see attached igv image for an example.

Anyone out there to understand what is going on and any way to resolve it?

Reads are mapping sporadically and we can see split reads as well, so it is not from DNA. Also, we use DNase. It is not annotation related either, as we have tried data from three major centers, ie, Ensembl, UCSC and NCBI using three different genome versions. We got a similar result, even remaking the library won't help.

Any suggestions?

Attached Images
File Type: png igv_snapshot.png (127.0 KB, 9 views)
dkumar is offline   Reply With Quote

exons location, read-mapping, rna-seq analysis

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 04:41 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO