Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by sgcsd View PostThank you vivek.
So what I understood is run the SNP pipeline for both WT and mutant the same way and after we get the SNP file filter the common ones and focus on the SNPs different in both.
Leave a comment:
-
Thank you vivek.
So what I understood is run the SNP pipeline for both WT and mutant the same way and after we get the SNP file filter the common ones and focus on the SNPs different in both.
Leave a comment:
-
I think you'd go through the SNP calling in the same way for both sets of samples. (i.e.., mapping to reference genome and calling SNPs using GATK/Samtools etc).
Then you could look at the common SNPs in dbSNP for the wild type strain and flag them in your wildtype variant files as being down to strain difference and proceed with the analysis for the remaining variants.
Leave a comment:
-
SNP calling from multiple genotypes
Hi
I am new to snp discovery analysis. We recently sequenced a wild type and two mutant lines using illumine. The wild type is different from the reference genome available. Can anyone suggest a pipeline for identifying the SNPs in WT-Mutant.
Do we need to assemble our WT before calling SNPs in mutant or can we use the reference genome to map the reads from both the WT and mutant and call the SNPs.
Appreciate your help.
Thank you
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, 03-27-2024, 06:37 PM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
03-27-2024, 06:37 PM
|
||
Started by seqadmin, 03-27-2024, 06:07 PM
|
0 responses
11 views
0 likes
|
Last Post
by seqadmin
03-27-2024, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
53 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: