User: roll

gravatar for roll
roll240
Reputation:
240
Status:
Trusted
Location:
United Kingdom
Last seen:
3 years, 11 months ago
Joined:
6 years, 2 months ago
Email:
s********@gmail.com

about me

Posts by roll

<prev • 80 results • page 1 of 8 • next >
8
votes
1
answer
19k
views
1
answer
converting vcf file to plink ped/map format while filtering the snps
... Hi, I was working on converting my vcf file into plink ped/map format. I used the following command from vcftools     vcftools --vcf myvcf.vcf --plink --out myplink I also would like to filter my snps based on minor allele frequency (maf). I was wondering whether simply using     vcftools --vc ...
plink map ped vcftools written 4.1 years ago by roll240 • updated 4.1 years ago by chrchang5234.2k
2
votes
1
answer
1.4k
views
1
answers
Answer: A: Bedtools subtract not dealing well with large datasets
... bedtools intersect -v ...
written 4.5 years ago by roll240
3
votes
1
answer
1.4k
views
1
answer
Bedtools subtract not dealing well with large datasets
... I am using bedtools subtract with large datasets and it keeps crashing, giving the following error     terminate called after throwing an instance of 'std::bad_alloc' Is there a way to get over this problem in bedtools?   Alternatively is there any other way to find nonoverlapping regions for tw ...
bedtools software error written 4.5 years ago by roll240
0
votes
4
answers
1.6k
views
4
answers
Comment: C: Count Columns For Each Window
... yes you can have more than 1. The example you are giving is correct. ...
written 4.7 years ago by roll240
0
votes
4
answers
1.6k
views
4
answers
Comment: C: Count Columns For Each Window
... yes exactly. My attempt was to have a list of all the windows and use while loop in perl. And awk to count the counts. But it is very slow. ...
written 4.7 years ago by roll240
7
votes
4
answers
1.6k
views
5 follow
4
answers
Count Columns For Each Window
... I would like to count columns for the matching windows (that is in bed format). I tried awk but too slow. For example, I have the following two windows chr1:100-1000 chr1:1500-3000 Fort these 2 windows I found the following matches and would like to count 6th column based on whether the last col ...
awk written 4.7 years ago by roll240 • updated 4.7 years ago by dariober9.7k
8
votes
3
answers
2.4k
views
13 follow
3
answers
How To Intersect A Range With Single Positions
... Hi, Is there any tool that will find whether a position fall into a certain region other than awk or bedtools intersect? That is, lets's assume i have a range with position chr1:10000-20000 and i have a list of positions chr1 100 1 2 3 chr1 12000 1 2 3 chr1 15000 1 2 3 chr1 25000 1 2 3 So ...
bed intersect written 4.7 years ago by roll240 • updated 4.7 years ago by Neilfws48k
0
votes
1
answer
1.7k
views
1
answers
Comment: C: Skipping Reads Bowtie
... Thanks. that make sense. I went through the bowtie parameter options but did not find which one would discard these. Do you know the name or which parameter i should set? ...
written 4.7 years ago by roll240
3
votes
1
answer
1.7k
views
1
answer
Skipping Reads Bowtie
... Hi, I have a question about the alignment of chip-seq data. I have got sample with 100 bp reads. After QC and trimming, these got shorter. I used bowtie to do the alignment. I got lots of warning message like Warning: Skipping read (myData.110237305 VADER:39:C0NL4ACXX:1:2316:19783:100655 length=1 ...
chip-seq bowtie written 4.7 years ago by roll240 • updated 4.5 years ago by Biostar ♦♦ 20
0
votes
1
answer
2.6k
views
1
answers
Comment: C: Comparing Two Bam Files Obtained From The Same Files And The Exact Settings
... this looks like a nice tool. I will try it. ...
written 4.8 years ago by roll240

Latest awards to roll

Popular Question 3.9 years ago, created a question with more than 1,000 views. For Does The Fastx_Toolkit Work On Gzip Compressed Files?
Scholar 4.5 years ago, created an answer that has been accepted. For A: Bedtools subtract not dealing well with large datasets
Student 4.6 years ago, asked a question with at least 3 up-votes. For How To Detect Contamination Or Sample Preparation Artifacts In Sequencing Results

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2209 users visited in the last hour