User: greyman

gravatar for greyman
greyman80
Reputation:
80
Status:
Trusted
Location:
Last seen:
1 week, 2 days ago
Joined:
9 months, 1 week ago
Email:
w*********@gmail.com

Posts by greyman

<prev • 20 results • page 1 of 2 • next >
0
votes
0
answers
101
views
0
answers
VQSR with extremely low TPs (<0.01), How low can tranche goes?
... Hi, Sorry that i have posted this at here because for some unknown reason i am unable post a question in GATK forum. Any help from here is truly appreciated. I have 45108 variants from 31 exome vcf files. After VariantRecalibrator, my tranche specificity shows the best Ti/Tv ratio at 57.8 (with Ti ...
exome vqsr gatk4 snp written 28 days ago by greyman80 • updated 28 days ago by ATpoint15k
0
votes
0
answers
114
views
0
answers
Comment: C: How to create 1000G_phase1.snps.high_confidence.hg19.sites.vcf ?
... Thank you for the recommendation. ...
written 7 weeks ago by greyman80
1
vote
0
answers
114
views
0
answers
How to create 1000G_phase1.snps.high_confidence.hg19.sites.vcf ?
... Hi, i am new to bioinformatics. Wondering how "1000G_phase1.snps.high_confidence.hg19.sites.vcf" is built (what makes it having high confidence?) and hope that i could get some advice on the pipelines to create one for phase 3 version. Thank you! ...
#gatk snp written 7 weeks ago by greyman80
1
vote
1
answer
212
views
1
answers
Comment: C: Colour doesn't change in Manhanttan plot.
... thank you, as i have just figured out the answer, should i close this question? ...
written 3 months ago by greyman80
3
votes
1
answer
212
views
1
answers
Answer: A: Colour doesn't change in Manhanttan plot.
... I have figured out the answer. Made a mistakes by using `out$SNP` for highlighting the SNP. Below means highlight all the SNPs form `out` dataframe input, not what I needed: highlight = out$SNP And should be just a character vector of SNPs that need highlighting, for example.: highlight ...
written 3 months ago by greyman80 • updated 3 months ago by zx87547.1k
5
votes
1
answer
212
views
1
answer
Colour doesn't change in Manhanttan plot.
... Below is my R scripts for the manhanttan plot, many similar forums has used the same codes for their manhattan plot, but it seems doesnt work for me. Also, the default colour supposed to be black/grey but it turned green in my plot, may i know what mistakes i have made? manhattan(out, chr="CHR" ...
R qqman manhattanplot gwas written 3 months ago by greyman80 • updated 3 months ago by zx87547.1k
0
votes
1
answer
479
views
1
answers
Comment: C: Can we find SNP from fasta sequences ?
... As i wanted to extract the sequence region with SNP from exome data, is there anyway to do it from fastq? Last time when i use fasta i extract the gene sequence from whole genome data that has been split into gene data ...
written 9 months ago by greyman80
6
votes
1
answer
479
views
6 follow
1
answer
Can we find SNP from fasta sequences ?
... I found the SNP from bam file and vcf workflow however I would like to try using FASTA for this process. Can we get Fasta format works? ...
fasta snp written 9 months ago by greyman80
0
votes
1
answer
462
views
1
answers
Comment: C: How to work with 2.6 TB genome data which is deposited in the server?
... Thanks genomax!! i would like to work on all data in once but it seems like i have to separate them into batch ...start searching about dual socket workstation like HP Z820 Tower Workstation 16-Core E5-2670 (16 cores, hard disk storage15TB, RAM32 GB).... and looks like i ll have to add more RAM to ...
written 9 months ago by greyman80
0
votes
1
answer
462
views
1
answers
Comment: C: How to work with 2.6 TB genome data which is deposited in the server?
... They dont own a HPC but they are interested to do modification to a Lenovo desktop that i m currently using. The 7k dollar would be invested in the modification, however, i ll request for more fund if buying a new desktop is necessary. They are expecting to see some fruitful output from the 2.6TB be ...
written 9 months ago by greyman80

Latest awards to greyman

Scholar 3 months ago, created an answer that has been accepted. For A: Colour doesn't change in Manhanttan plot.
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Colour doesn't change in Manhanttan plot.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1421 users visited in the last hour