User: gokberk

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gokberk60
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Posts by gokberk

<prev • 33 results • page 1 of 4 • next >
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Comment: C: Phylogenetic tree construction from small sized SNP data
... Yes, it worked, thanks a lot Philipp! ...
written 10 weeks ago by gokberk60
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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 10 weeks ago by gokberk60 • updated 10 weeks ago by Philipp Bayer6.4k
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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 11 weeks ago by gokberk60
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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 11 weeks ago by gokberk60
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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 11 weeks ago by gokberk60
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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 11 weeks ago by gokberk60
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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 3 months ago by gokberk60
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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 3 months ago by gokberk60
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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 3 months ago by gokberk60
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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 3 months ago by gokberk60

Latest awards to gokberk

Scholar 3 months ago, created an answer that has been accepted. For A: Long-read alignment with Minimap2
Supporter 4 months ago, voted at least 25 times.

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