Tweet
reads mapping to overlapping genes?
Many reads are mapped to positions where overlapping genes reside. So we overestimated the number of reads mapping to some genes. How to deal with this problem?
Thank you for your time!
-
Many reads are mapped to positions where overlapping genes reside. So we overestimated the number of reads mapping to some genes. How to deal with this problem?
Thank you for your time!
-
It depends on the structure of the genes, but we've started calculating our counts as bp of read per kbp of transcript, but calculating this value separately for every exon, and then taking the mean or median value of all exons as the overall value for the gene. This seems to cut down on problems which only affect a small part of the gene.Originally posted by beliefbio View Post
Many reads are mapped to positions where overlapping genes reside. So we overestimated the number of reads mapping to some genes. How to deal with this problem?
Thank you for your time! -
Yes, this should also reduce the impact of alternative splicing. One question: if different transcripts use the same exon, do you count the corresponding value several times when computing the mean or median, or just once?Originally posted by simonandrews View PostComment
-
Take a look at our read counter tool that does not count read-pairs mapped to the same-strand overlapping part of genes: http://seqanswers.com/forums/showthread.php?p=134850
https://code.google.com/p/recog/Comment
-
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...Today, 07:48 AM -
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM
Comment