Can anyone recommend a good tool to display a coverage plot over a chromosome? The images produced by UCSC aren't of great quality nor can I customize it. I'm curious what most people use to generate high quality coverage plots with.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Maybe the alignment view of IGV is enough for want you want, it has a coverage track:
If you are unable to find something or have a question about our new website, please email [email protected]. For other inquiries related to the Broad Institute, the necessary contact information can be found here.
For a completely different idea you could also have a look at (the R package for) Hilbert curves:
Comment
-
Savant can do that as well. If've got a BAM file of your aligments you can convert it into a BAM Coverage files. That allows you to display coverage along a chromosome easily. I attached a picture of a whole human chromosome 1 coverage plot.
Hope that helps,
Best regards,
PeterAttached Files
Comment
-
Originally posted by svl View PostMaybe the alignment view of IGV is enough for want you want, it has a coverage track:
If you are unable to find something or have a question about our new website, please email [email protected]. For other inquiries related to the Broad Institute, the necessary contact information can be found here.
For a completely different idea you could also have a look at (the R package for) Hilbert curves:
http://www.ebi.ac.uk/huber-srv/hilbert/--
bioinfosm
Comment
-
IGV does a great job of displaying coverage information, but you do need to zoom in enough. I want something more on the chromosome level to get an overview of my coverage.
Thank you for all the suggestions. I'll have to spend some time looking at these.
Comment
-
hi, simonandrews
Do you have any experience in trying SeqMonk in linux? I use SSH to connect our linux server. I just downloaded SeqMonk to my directory and tried to launch it by using
java -Xmx1500m -classpath $CLASSPATH:. uk.ac.bbsrc.babraham.SeqMonk.SeqMonkApplication
Thanks
-c
Comment
-
-
Are you using Windows? You'll need to install an X Server like ReflectionX, eXceed, or Cygwin. Googling for "X Forwarding on Windows" turned up http://www.cs.caltech.edu/courses/cs.../xwindows.html
Comment
-
Originally posted by cliff View Posthi, simonandrews
Do you have any experience in trying SeqMonk in linux?
As others have pointed out, if you want to run SeqMonk on linux from a remote system over SSH you'll need to make sure that your ssh session is started with an X tunnel available (either ssh -X or set the appropriate flags in PuttY) and that you have a local X server running on your machine. This is the same for all graphical linux programs.
Having said that, I'm not sure I'd encourage people to run SeqMonk this way. The nature of the program means that it does big complex updates to its display all the time, which means that it has to send an awful lot of display data over X to work remotely. We know of one site who do it this way, but they run an nx server to improve the display performance.
Really, SeqMonk is better run as a local native application. It's designed to work on modest hardware so you don't need a particularly powerful PC to run it (the default configuration is optimised for a dual core machine with 2GB of RAM). If you've not tried running it directly on your desktop I'd try that before going to the hassle of getting a decent remote connection working.
Comment
-
Hi everyone,
IGV can also visualize the coverage of a whole chromosome at once without having to zoom in:
You need to create an extra .tdf-file (a binary tiled data file) using igvtools with the command "count" (see http://www.broadinstitute.org/igv/igvtools).
For example
igvtools count -z 7 -w 25 -e 0 alignments.bam alignments.coverage.tdf hg19
It supports the formats .sam, .bam, .aligned, .sorted.txt, and .bed.
Then you can load the .tdf-file into IGV and you get a pretty nice coverage plot.Last edited by ForeignMan; 09-30-2010, 12:00 AM.
Comment
Latest Articles
Collapse
-
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 -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:37 PM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
49 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
67 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment