Could any one suggest me how to create a circular genome map with read coverage track. Thanks in advance.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
-
Circos is probably the most commonly used one.
Others include
CGview (http://wishart.biology.ualberta.ca/cgview/)
DNAPlotter (http://bioinformatics.oxfordjournals.../25/1/119.full)
GenomeViz (http://www.biomedcentral.com/1471-2105/5/198)Marco
Comment
-
BRIG looks quite nice, haven't used it yet though
Download BLAST Ring Image Generator for free. BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402.
Comment
-
BUMPED.
Thank you for this. We're using CLC Bio for routine analysis (which is really nice) but it doesn't support circular genome maps at the moment.
So far BRIG has done what I need. CIRCOS looks gorgeous, after 2 hours installing and configuring all the perl libraries needed to support it, I caved and gave up. Maybe I try again in a week or so.
Comment
-
circos
I have to plot a seq uencing data in circle and wonder what tool wil be used. I found Circos but is not window based and intutive for a biologist. Is there a version of CIRCOS which can be easily used or any alternative tool. It is a human genome based data.
Thanks
Comment
-
Regarding DNAplotter
Hello everyone
I have done re-sequencing of one of Vibrio cholerae strain and has data in form of consensus sequence for both the chromosomes. Now I want to make these consensus circular and compare them with the reference . Is it possible to do that with DNAplotter? I mean I want that outer circle should be my reference sequence and the inner circle should me my consensus sequence.
I am trying to use DNAplotter but not getting much. please pardon me if I am missing something very obvious.
Regards,
NehaLast edited by neha; 07-19-2012, 09:16 PM.
Comment
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
29 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment