User: gokberk

gravatar for gokberk
gokberk60
Reputation:
60
Status:
Trusted
Location:
Last seen:
6 days, 18 hours ago
Joined:
1 year, 3 months ago
Email:
g*************@gmail.com

Posts by gokberk

<prev • 33 results • page 1 of 4 • next >
0
votes
1
answer
470
views
1
answers
Comment: C: Phylogenetic tree construction from small sized SNP data
... Yes, it worked, thanks a lot Philipp! ...
written 12 months ago by gokberk60
2
votes
1
answer
470
views
1
answer
Phylogenetic tree construction from small sized SNP data
... Hi all, I should construct a phylogenetic tree using a subset of SNPs hitting a certain gene. I tried `SNPhyl`, but my vcf file is basically too small for this tool to run and I received the following error: VCF file (../../../Data/nanog.vcf) is too small to run this script! So, I was wonderi ...
phylogenetic tree snp snphyl written 12 months ago by gokberk60 • updated 12 months ago by Philipp Bayer6.7k
0
votes
1
answer
276
views
1
answers
Comment: C: Missing variants in hg38 lift-over of 1000-genomes data
... Oh, didn't know that direct hg38 calls were available. It looks like they have all SNPs that were missing in the lift-over indeed. Thanks a lot genomax! ...
written 12 months ago by gokberk60
2
votes
1
answer
276
views
1
answer
Missing variants in hg38 lift-over of 1000-genomes data
... Hi everyone, I've been looking in the hg38 mapped version of chromosome 12 from 1000 genomes (phase 3) data. Curiously, at certain parts (longer than several hundred kb) of this lift-over version, there are not any SNPs. The region I'm interested in is chromosome 12: 7,500,000-8,000,000. When I run ...
vcf 1000genomes written 12 months ago by gokberk60
1
vote
0
answers
305
views
0
answers
Comment: C: Extracting super-population allele frequencies from 1000 genomes (phase 3) data
... Thanks Shicheng. I've just managed to do it using `bcftools query`. In case someone needs it, here is the command I used: bcftools query -f '%CHROM %POS %EAS_AF %AMR_AF %AFR_AF %EUR_AF %SAS_AF \n' myFile.bcf ...
written 12 months ago by gokberk60
4
votes
0
answers
305
views
0
answers
Extracting super-population allele frequencies from 1000 genomes (phase 3) data
... Hi all, I'm interested in super-population level allele frequencies of SNPs on a gene. I cropped my variants of interest and made a smaller vcf file. Now, I'd like to extract the allele frequencies for these variants. I've been following the instructions [here][1], even though it gives a "micro-po ...
vcf 1000genomes written 12 months ago by gokberk60
0
votes
1
answer
1.3k
views
1
answers
Comment: C: Long-read alignment with Minimap2
... I tried that but since the genome is about 2.8 GB, I could not manage to upload it and received errors even though I tried multiple times. ...
written 13 months ago by gokberk60
2
votes
1
answer
1.3k
views
1
answers
Answer: A: Long-read alignment with Minimap2
... I guess my query sequence was not formatted as a proper fasta file, I fixed it and problem is solved now, sorry for bothering :). ...
written 13 months ago by gokberk60
5
votes
1
answer
1.3k
views
1
answer
Long-read alignment with Minimap2
... Hi all, I want to align the coding sequence of a gene (which I cropped out from hg38) to genomic read contigs of a non-human ape. All contigs are in a single fasta file (2.8 GB) and the length of the coding sequence that I want to align to it is ~400 bp. I've been using Minimap2, here is my command ...
minimap2 long-read dna-seq written 13 months ago by gokberk60 • updated 4 months ago by Biostar ♦♦ 20
0
votes
0
answers
601
views
0
answers
Comment: C: Extracting uniquely mapped reads from bams
... Thanks for your responses Nitin and ATpoint. I've already seen the thread ATpoint mentioned, however the suggested code there gave me an empty bam file for some reason. That's why I opened a new issue. And on top of that, I was hoping to find some suggestions for mapping RNA-seq reads to a gene and ...
written 13 months ago by gokberk60

Latest awards to gokberk

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Problem with generating BAM files with STAR
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Long-read alignment with Minimap2
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Long-read alignment with Minimap2
Scholar 13 months ago, created an answer that has been accepted. For A: Long-read alignment with Minimap2
Supporter 13 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1182 users visited in the last hour