Would wiggle plots be appropriate for your uses? They are at least supported by GBrowse (and likely other programs):
Here's an example of GBrowse use, where the density is used to change the colour (rather than the thickness) of the line:
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Hi, can you expound on what new information you would glean from such a view that you don't already get in a coverage plot? There is a little extra information there, but is not clear what would be important.
Also, how do you define an identical read, same bases or just same position?
Leave a comment:
-
yes Jim, anything approximate would be fine..like you are implying one could be on a log-scale for instance... the scale can be given to the browser in a bed file, the browser just needs to collapse and weight the "number of reads" given to it (the number could be log of the actual reads) .. i am happy to play around with the scale, i just need a browser with that feature.
Leave a comment:
-
Hi, its an interesting idea but might be difficult in practice. Would you distinguish between 10 reads, 100 reads, and 1000 reads?
Jim
Leave a comment:
-
weighted read display - genome browser
Hi,
does anyone know of a genome browser that collapse all exact reads to one read, but with a thickness or color that can reflect the number of reads for that loaction?
in other words if i have a genomic location say 1-50 that has 200 reads and another location with 3-75 with 20 reads, i would like to see a longline for 1-50 location with a very thickline (or an appropriate color), while 3-75 gets a much smaller thickness? Can UCSC do this? anyother favorites you know for bed file visulaization witht this purpose?
something like
___________________________
___________________________
___________________________ for 1-50
___________________________________ for 3-75
thanks
svmTags: None
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
11 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
51 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
68 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Leave a comment: