Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • dkumar
    started a topic RNA-seq data not mapping to exon

    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?

    Thanks,
    Dibyendu
    Attached Files

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 07:15 AM
0 responses
5 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 10:28 AM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 07:35 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-22-2024, 02:06 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Working...
X