It seems that as methods improve, and more data is collected migrating an older version of an assembly to a newer version can become necessary, assuming that an assembly has been adopted and manually annotated with experiments. I am wondering what the existing strategies are for doing this?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by SES View PostThere is a LiftOver tool from UCSC for that (I recall that the same tool may be available from Galaxy).
Also are there any other strategies out there. UCSC sites GRIMM, which seems a little naive.
Comment
-
Originally posted by rskr View PostI am more interested in how they generate the liftOver coordinates than the liftOver itself, and there is some documentation of that.
Also are there any other strategies out there. UCSC sites GRIMM, which seems a little naive.
Comment
-
Originally posted by SES View PostSo you are not actually interested in the coordinates? Sorry but it's not clear what you are trying to do.
Comment
-
Okay, I thought you were dealing with an annotation file but it sounds like you are talking about comparing actual assemblies. If you are not trying to combine the assemblies but just find where the annotations are in the second assembly, why not just use vmatch or MUMmer to see where the contigs from assembly 1 are in assembly 2. The annotation coordinates would change but they would not get lost because you can easily keep track of where every contig matches.
Comment
-
Originally posted by SES View PostOkay, I thought you were dealing with an annotation file but it sounds like you are talking about comparing actual assemblies. If you are not trying to combine the assemblies but just find where the annotations are in the second assembly, why not just use vmatch or MUMmer to see where the contigs from assembly 1 are in assembly 2. The annotation coordinates would change but they would not get lost because you can easily keep track of where every contig matches.
Comment
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:57 AM
|
0 responses
11 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:57 AM
|
||
Started by seqadmin, 05-06-2024, 07:17 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
05-06-2024, 07:17 AM
|
||
Started by seqadmin, 05-02-2024, 08:06 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-02-2024, 08:06 AM
|
||
Started by seqadmin, 04-30-2024, 12:17 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-30-2024, 12:17 PM
|
Comment