SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
CNV analysis from Exom-seq data younko Bioinformatics 0 06-09-2014 12:28 AM
Public Mouse Methyl-seq Data? serenaliao Epigenetics 4 02-27-2013 12:57 AM
mouse ENCODE transcription factor ChIP-seq data gene_x Bioinformatics 1 02-04-2013 10:22 PM
mouse embryonic stem cell RNA-Seq data kykwan Bioinformatics 1 10-19-2011 09:19 PM
mouse bone marrow rna-seq data keithforest General 1 02-25-2011 09:49 AM

Reply
 
Thread Tools
Old 07-16-2014, 12:35 PM   #1
arcolombo698
Senior Member
 
Location: Los Angeles

Join Date: Nov 2013
Posts: 142
Default Cnv-seq On Mouse Data

Hi, I am interested in using CNV-seq on mm10, however, when I use the command line the genome for mouse is not avail... is this CNV-seq software not useful for mm10 ref genomes?


--genome = (human, chicken, chrom1, autosome, sex, chromX, chromY)
(higher priority than --genome-size)
arcolombo698 is offline   Reply With Quote
Old 07-16-2014, 05:00 PM   #2
arcolombo698
Senior Member
 
Location: Los Angeles

Join Date: Nov 2013
Posts: 142
Default

What I did was under --genome command, I included the same fasta file used for alignment of the mouse genome.

However, I am not sure this is allowed. I know for RDxplorer, the manual says that it is for HUMAN ONLY.

Has anyone used CNV-seq on mm10 reference genome?
arcolombo698 is offline   Reply With Quote
Old 07-01-2015, 09:59 AM   #3
vbajic
Junior Member
 
Location: Europe

Join Date: Jul 2015
Posts: 2
Default

Quote:
Originally Posted by arcolombo698 View Post
is this CNV-seq software not useful for mm10 ref genomes?
(higher priority than --genome-size)
It is useful for mm10. In the manual it is written that either --genome or --genome-size option must be specified. So if you know genome size you can set up that one. However, I am not sure if that would work if you are using the whole genome with all chromosomes (since you are entering in --genome-size just one number and program needs to know size of each chromosome). I am working just on one chromosome and I set up --genome-size. I didn't upload any fasta file.
vbajic is offline   Reply With Quote
Reply

Tags
cnvseq

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 11:51 AM.


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