I am trying to count short tandem repeats (STR) from 1000 Genomes Project data using the low coverage BAM files, but am getting the same repeats even on known fast STRs. Should I be looking at other files within the project to do this? I am using SAMTools.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Depending on the aligner & parameters used, these may not have aligned well. In the worst case, no single read can contain the entire repeat array AND unique sequence on either side to enable conclusive mapping -- even if the repeat is not strictly too long, very long repeats will be unlikely to have randomly fragmented in such a manner that they can be uniquely mapped.
STRs are definitely findable in the Watson & Venter BAM files & you might test out your method there. These were done with long read (454 & Sanger respectively) technologies that can read through all but the most ginormous repeats.
My intern last summer developed a tool for this purpose; anyone interested in beta testing it can PM me about access. I'm trying to get some additional data generated to test it prior to releasing & publishing it -- the problem is a dearth of data in which the actual repeat length is known as tested by conventional methods. I know we looked at 1K genome data & thought she was able to pull variation out, but I'd need to check.
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
67 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment