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Search: Posts Made By: Jayakumar S
Forum: Bioinformatics 09-04-2019, 02:48 AM
Replies: 0
Views: 809
Posted By Jayakumar S
STATISTICAL TEST FOR SNPs

Dear All,
Can anyone suggest some statistical tests to check whether the identified SNPs from the whole genome are significant?

Thank you
Forum: Bioinformatics 05-02-2019, 05:49 AM
Replies: 2
Views: 1,360
Posted By Jayakumar S
Thank you for your response and suggestions. They...

Thank you for your response and suggestions. They are closely related species but vary in their chromosome number. My idea is to go for reference guided donovo assembly. Kindly suggest about the...
Forum: Bioinformatics 05-01-2019, 11:32 PM
Replies: 2
Views: 1,360
Posted By Jayakumar S
Reference based genome assembly

Hi,
I am going to have the paired end reads from Illumina as well from Pac-bio for genome of about 3 gb.
Can anyone suggest various tools for the reference based genome assembly?
Kindly suggest...
Forum: Bioinformatics 12-04-2016, 04:30 PM
Replies: 4
Views: 1,751
Posted By Jayakumar S
Thank you for the suggestion. Will try for that...

Thank you for the suggestion.
Will try for that and let you know.

Jayakumar S
Forum: Bioinformatics 12-02-2016, 08:53 PM
Replies: 4
Views: 1,751
Posted By Jayakumar S
Genome alignment

Hi,
Planning to align the scaffolds with the reference genome already available. The size of the reference genome is about 3 gb.
Kindly suggest any suitable methods/softwares for the same....
Forum: Bioinformatics 10-15-2016, 10:15 PM
Replies: 0
Views: 863
Posted By Jayakumar S
Primer designing for the SSR markers

Hi All,
I have used the contigs of a genome to identify the SSR markers using the MISA tool. But was not able to proceed further for identification of the primers for all the markers that has been...
Forum: Bioinformatics 05-06-2016, 11:41 PM
Replies: 0
Views: 842
Posted By Jayakumar S
Scaffold & chromosome number

Hi All,
I am presently working in Yak.
When I mapped the ddRAD sequence reads to the reference genome, got the information regarding the scaffold number where the reads matches, its position and...
Forum: Bioinformatics 04-19-2016, 04:05 AM
Replies: 1
Views: 1,986
Posted By Jayakumar S
DArT seq vs GBS & ddRAD

Hi,
Can anyone update me about the difference between the DArT seq vs GBS & ddRAD.
DArT array is for studying the expression pattern.
Also let me know which method is found to be more useful for...
Forum: Bioinformatics 03-26-2016, 04:06 AM
Replies: 0
Views: 1,118
Posted By Jayakumar S
ddRAD

Hi,
Recently got the ddRAD sequence data of yak from the Illumina service providers.
Wish to know if any of you are working in cattle or yak using ddRAD?
Also, eager to know about the experience...
Forum: Bioinformatics 01-12-2016, 05:13 PM
Replies: 0
Views: 984
Posted By Jayakumar S
Bovine HD SNP chip - data filtration

Hi,
Got the final report of Bovine HD SNP chip results from illumina. Also got thee .ped and .map files.
Its having the genotyping results of the SNPs present in all the autosomes as well as the...
Forum: Bioinformatics 07-01-2015, 04:05 AM
Replies: 0
Views: 864
Posted By Jayakumar S
HD SNP chip data

Hi,
We have received the HD SNP chip data from the Illumina service providers.
We don't have the genome studio software to read the raw data and convert the same to Plink format.
Is there any open...
Forum: Bioinformatics 05-19-2015, 09:33 PM
Replies: 0
Views: 659
Posted By Jayakumar S
SNP chip dataset - How to read?

Hi,
We have received the data of SNP Chip in .txt format from Illumina service providers.
We don't have the Genome Studio software to open the same.
Kindly suggest about the open source tools that...
Forum: Bioinformatics 05-15-2015, 06:21 PM
Replies: 2
Gbs
Views: 1,396
Posted By Jayakumar S
SNPsaurus, Thank you for the response and the...

SNPsaurus,
Thank you for the response and the details.

Jayakumar S
Forum: Bioinformatics 05-15-2015, 01:45 AM
Replies: 2
Gbs
Views: 1,396
Posted By Jayakumar S
Gbs

Hi,
Can we be able to identify the heterozygous genotypes by GBS when we do compare with reference sequence?

Thanks
Jayakumar S
Forum: Bioinformatics 04-30-2015, 10:01 PM
Replies: 3
Views: 1,229
Posted By Jayakumar S
GBS by Hiseq & NGS

Thanks for your response.
Forum: Bioinformatics 04-30-2015, 12:19 AM
Replies: 3
Views: 1,229
Posted By Jayakumar S
GBS by Hiseq & NGS

Hello,
Can anyone give me some insight into GBS by NGS as well by Hiseq?.

Thanks
Jayakumar S
Forum: Bioinformatics 09-29-2014, 09:30 PM
Replies: 0
Views: 998
Posted By Jayakumar S
GBS/ddRAD in livestock

Hi,
Can you share your experience of ddRAD/GBS in livestock to study their diversity?.
Also, suggest me the suitable pipeline (TASSEL, STACKS, etc) to be used for the analysis?.

Thanks...
Forum: Bioinformatics 09-26-2014, 09:58 PM
Replies: 5
Views: 5,140
Posted By Jayakumar S
Thank you for the information. Can you please...

Thank you for the information.
Can you please suggest whether ddRAD or GBS will be better to study the diversity in livestock?.

Thanks
Jayakumar S
Forum: Bioinformatics 09-26-2014, 03:40 AM
Replies: 5
Views: 5,140
Posted By Jayakumar S
Hi, I understand that the number of SNPs that...

Hi,
I understand that the number of SNPs that can be genotyped is not dependent on the techniques.
For the specified number of SNPs identified at 20X, in which technique, we will get more number of...
Forum: Bioinformatics 09-25-2014, 03:41 AM
Replies: 5
Views: 5,140
Posted By Jayakumar S
GBS vs RAD

Hello,
We are planning to study the diversity of a species and for the same we are in a confusion whether to go for RAD or GBS?.
In which technique, we will get more SNPs genotyped?.
What will be...
Forum: Bioinformatics 06-01-2014, 05:58 AM
Replies: 6
Views: 1,237
Posted By Jayakumar S
Yes, it may be the reason. Thank you for the...

Yes, it may be the reason.
Thank you for the suggestion.
Will try the way that you have suggested.
Forum: Bioinformatics 06-01-2014, 05:51 AM
Replies: 6
Views: 1,237
Posted By Jayakumar S
Thank you for providing me with the link. Every...

Thank you for providing me with the link.
Every time, I am getting the network error.
But, still trying.

Thanks
Forum: Bioinformatics 06-01-2014, 05:22 AM
Replies: 6
Views: 1,237
Posted By Jayakumar S
I am trying with the link that you have provided....

I am trying with the link that you have provided.
But, it seems it will take so long time.

Jayakumar S
Forum: Bioinformatics 06-01-2014, 01:51 AM
Replies: 6
Views: 1,237
Posted By Jayakumar S
Bos taurus 3.1 version

Hello,
I am trying to download the annotated version of Bos taurus 3.1 version assembly. But, I was not able to do so.
How to proceed with this?. Please let me know.

Thanks
Jayakumar S
Forum: Bioinformatics 05-19-2014, 03:17 AM
Replies: 13
Views: 2,341
Posted By Jayakumar S
Thanks Ryan for all the clarification. ...

Thanks Ryan for all the clarification.

Jayakumar S
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