SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Genome size and corrected genome size priya Bioinformatics 7 03-25-2015 02:13 PM
Calculating Sample Size Estimates for RNA Sequencing Data RockChalkJayhawk RNA Sequencing 3 12-06-2013 10:57 AM
RNA-Seq: Calculating Sample Size Estimates for RNA Sequencing Data. Newsbot! Literature Watch 0 08-22-2013 07:20 AM
Which .fa files should I include when creating a ref. genome of a non-human species? Stina Bioinformatics 3 11-29-2012 12:50 AM

Reply
 
Thread Tools
Old 03-21-2015, 11:01 AM   #1
bzotter
Junior Member
 
Location: New York

Join Date: Mar 2015
Posts: 1
Default Include heterochromatin in genome size estimates?

I am planning on sequencing several entire drosophila (fruit fly) genomes for an upcoming project. The published length of the drosophila genome is ~150 Mbp, up to ~175 Mbp including known heterochromatin. However, there is supposedly another 25-50 Mbp of heterochromatin in the form of large peri-centromeric and per-telomeric DNA satellites that is not included in these estimates.

My question is, how much does heterochromatin factor in to coverage calculations for NGS? When I am calculating my estimated genome coverage and figuring out how many lanes we need, should I be using 150 Mbp (eurchromatin only) or ~200 Mbp (euchromatin+heterochromatin)? I know that large tandem repeats and "structural" DNA (i.e. satellites) will not be properly amplified or sequenced, but I'm assuming they will still consume reagents and take up some space in the lane. Any advice you can provide would be much appreciated.

The sequencing will be done on an illumina HiSeq 2500, most likely using 2*100 bp reads.

Thanks,
Brendan
bzotter is offline   Reply With Quote
Reply

Tags
drosophila, heterochromatin, illumina, whole genome sequencing

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 03:30 PM.


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