User: waqasnayab

gravatar for waqasnayab
waqasnayab100
Reputation:
100
Status:
Trusted
Location:
Pakistan
Last seen:
1 week, 3 days ago
Joined:
1 year, 11 months ago
Email:
w*********@gmail.com

Posts by waqasnayab

<prev • 56 results • page 1 of 6 • next >
1
vote
3
answers
174
views
3
answers
Comment: C: Extract SNPs within 5 bps distance apart
... Yes, Pierre GATK's VariantFiltration worked for me. I wanted the exact same thing...,,,!!!! Big Thanks...,,,,!!!! Cheers, Waqas. ...
written 10 days ago by waqasnayab100
0
votes
3
answers
174
views
3
answers
Comment: C: Extract SNPs within 5 bps distance apart
... yeah, chromosomal positions (second column) is my target. I searched on google but I failed. Is there a way, to do the same in awk? Thanks, Waqas. ...
written 10 days ago by waqasnayab100
5
votes
3
answers
174
views
5 follow
3
answers
Extract SNPs within 5 bps distance apart
... Hi, I am wondering is there a way to extract / print those variants from a vcf file whose distance is not more than 5 bps apart? Regards, Waqas. ...
vcf R next-gen snp written 10 days ago by waqasnayab100 • updated 10 days ago by sacha710
0
votes
1
answer
137
views
1
answers
Comment: C: Match columns of two different files and paste a value of corrsponding match exi
... @Alex This really worked for me, although have some discrepancies in lines, but I managed at the end. Thanks Alex. Best, Waqas. ...
written 7 weeks ago by waqasnayab100
3
votes
1
answer
137
views
1
answer
Match columns of two different files and paste a value of corrsponding match existed in another column
... Hi, I have two files: file1: chr1 873251 0.0620 chr1 930248 0.9210 chr1 930939 0.2110 chr1 931131 0.6050 file2: chr1 873251 rs11240779 G A 4047.9 6 0.75 8 171 23.81 1.071 53.55 ncRNA_intronic 0 FA chr1 9302 ...
genome next-gen sequencing written 7 weeks ago by waqasnayab100 • updated 7 weeks ago by Alex Reynolds17k
0
votes
1
answer
246
views
1
answers
Comment: C: simple statistics of column values in different rows
... Thanks for links but the problem is to how to specify the line numbers whom I want to take the simple statistics??? ...
written 4 months ago by waqasnayab100
2
votes
1
answer
246
views
1
answer
(Closed) simple statistics of column values in different rows
... Hi, I'm wondering is there any unix command / tool to output mean, median, standard deviation, min, max, quartiles zones, etc of specific values grouped in a column: 38.35 37.42 36.64 36.56 36.28 36.78 36.98 36.52 36.17 35.00 34.84 35.24 35.86 ...
genome descriptive statistics next-gen sed awk written 4 months ago by waqasnayab100 • updated 4 months ago by Santosh Anand850
0
votes
0
answers
205
views
0
answers
MToolBox VCF output error
... Hi, Dear Community, I am unable to generate the the VCF file from MToolBox. However, except this I able to generate all the output files, including VCF_dict_tmp. When I run the command: MToolBox.sh -i ~/software/MToolBox-master/test_config.sh I got this error: .................. ...
software error next-gen snp written 4 months ago by waqasnayab100 • updated 3 months ago by Biostar ♦♦ 10
0
votes
1
answer
209
views
1
answer
WGS for mtDNA variation
... Hi, Dear Community, Could we use whole genome sequencing (WGS) data to detect / identify mitochondrial DNA (mtDNA) variation? Thanks, Waqas. ...
assembly snp sequencing written 5 months ago by waqasnayab100 • updated 5 months ago by WouterDeCoster15k
3
votes
0
answers
272
views
0
answers
Replacing column one values in R
... Hi, I want to replace column one values with **genome** string. I did the following: cvrge <- read.table("genome_cvrge_hist_nochr.txt") > head (cvrge) V1 V2 V3 V4 V5 1 1 0 36163905 249250621 0.1450910 2 1 1 7607795 249250621 0.0305227 3 1 ...
R next-gen alignment written 7 months ago by waqasnayab100

Latest awards to waqasnayab

Student 13 months ago, asked a question with at least 3 up-votes. For Donation of Old / Refurbished Computer Servers for setting up Bioinformatics Lab

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 698 users visited in the last hour