SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Genome size estimation moinul De novo discovery 9 04-04-2014 03:22 AM
DESeq: estimateSizeFactors, library size estimation Azazel Bioinformatics 7 02-18-2013 06:09 PM
Inquiry of Parsing tblastn result to get nucleotide sequence from the db file sunfuhui Bioinformatics 2 09-12-2012 05:39 AM
bwa insert size estimation athena.uci Bioinformatics 2 11-07-2011 08:49 AM
what is the file size for a 30X human genome sequencing file, raw and BAM? RNA-seq Illumina/Solexa 2 04-15-2011 11:27 AM

Reply
 
Thread Tools
Old 10-20-2013, 07:38 AM   #1
pcmount87
Junior Member
 
Location: US

Join Date: Oct 2013
Posts: 4
Default Inquiry regarding input file for genome size estimation by Jellyfish

Hi,

Do anybody mind to share that what is the "best" or "suitable" input file for genome size estimation program such as Jellyfish?

I still confuse should I used original raw sequencing read, pair-end data after preprocessing analysis (trim adaptor, remove low quality read, remove duplicate read, etc), or pair-end + single-end data after preprocessing analysis (trim adaptor, remove low quality read, remove duplicate read, etc)?

I have try the above 3 different data as an input file for Jellyfish by using 17-mer.
My data set is novel isolated bacteria.
Thus I not too sure what is the exact genome size.

The peak of 17-mer frequency (M) in reads is correlated with the real sequencing depth (N), read length (L), and kmer length (K), their relations can be expressed in a experienced formula: M = N * (L K + 1) / L.

All the above 3 different data set gives me different peak of 17-mer frequency.
Thus it effect the calculation of genome size too.

Thanks for any advice.
pcmount87 is offline   Reply With Quote
Reply

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 02:22 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO