Statistical analysis on tags mapping in binned chromosomes intervals
Hi!
I have a question related to this post:
My goal is to check whether different libraries have statistically significant differences int the density of mapped tags along the chromosomes.
I've binned the human chromosomes with bedtools makewindows, now I need to intersect the BED files derived from my libraries to these bins...but what would be the best tool/statistical analysis to test for differences in densities in each bin for different libraries?
Thank you in advance!
1 answer
Bioconductor edgeR and DESeq2 packages are built for doing just this. You can treat the bins as "genes" and just follow a normal rna-seq workflow.
• 0 views
•
link
updated
by
Ram
•
written
by
Sean Davis
•
written
by
Sean Davis
Log in to answer this question.
More posts like this
-
match bin number with the coordinate for each chromosome
written by mthm •
-
Mince a vcf into n bins of a given range
written by Noctiluca •
-
Taxonomic classification of MAGs
written by c.e.chong •
-
Stastical test for difference between TPMs for two transcript isoforms of a gene
written by jparker4 •
-
Get Reads from a Bin
written by irazoqui.matias •
-
Tool to compare whole genebody enrichment between different samples (MeDip-seq)
written by florian.noack •
-
Best approach to measure statistically significant difference between two regions in a gene
written by Nabeel Ahmed •
-
Intersect versus Count Overlapping Intervals
written by cellochick09 •
-
Genomic feature overlaps taking into account underlying sequence feature distributions
written by Sakti
-
Help With Multinomial Distribution Application To Genome Question
written by Wayne
