SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Accessing Genomic data in a large vcf.gz file XeroxHero69 Bioinformatics 12 05-06-2019 11:44 AM
Question on reads mapping smallRNA-seq (100% feature coverage) Liam_Gallagher Bioinformatics 0 04-20-2018 08:26 AM
feature coverage: + and - strands, overlaps Anna Nad General 0 11-12-2012 04:37 AM
"nucleotide coverage" to genome feature coverage sheremey Bioinformatics 3 11-02-2010 12:24 PM

Reply
 
Thread Tools
Old 10-25-2021, 12:52 AM   #1
marco12345
Member
 
Location: barcelona

Join Date: Mar 2013
Posts: 19
Question Coverage around genomic feature - large amount of data

Hi,

I have an alignment of human data (a small bam file with less than 1M reads), and would like to calculate and plot the coverage around specific genomic features.

Specifically, I would like to calculate coverage of 100Kbp before and after each Transcription Start Site (TSS). This can be made in windows of 1000bp. I tried different methods, mostly with R and GRanges, but couldn't get the results because of the dimension of the outputted files. The probelm is that all TSS are around 200'000, so you can imagine how gigantic the outputs are.
An average of of the values for each window will also work (i.e. for each 1Kbp window between +100Kbp and -100Kbp around each TSS, I can plot the average of all windows with the same distance from each TSS).

Are there any program or memory-saving methods to do this?

Thanks in advance.
marco12345 is offline   Reply With Quote
Reply

Tags
bam, coverage calculation, plotting, tss plot

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 03:06 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO