User: cetin.m

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cetin.m10
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Posts by cetin.m

<prev • 13 results • page 1 of 2 • next >
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Beagle permanent file
... I am running Beagle for imputation. I am in the process ofoptimizing it, so I have to run the program repeatedly with slightly different parameters. But I am using the same reference panel each time. I am wondering if the calculations made on this reference panel can be permanently written to the h ...
imputation beagle written 4 days ago by cetin.m10
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Comment: C: Beagle 4.1 imputation
... It is a server with 200BG ram. and here is the cpu: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit CPU(s): 32 Thread(s) per core: 2 Core(s) per socket: 8 Socket(s): 2 Model name: Intel(R) Xeon(R) CPU E5-2640 v2 @ 2.00GHz CPU M ...
written 6 days ago by cetin.m10
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bcftools 1.4.1 call parameters
... I first do samtools mpileup: samtools mpileup -uf /mnt/NAS/share/Ref/human/hs37d5.fa -l 1000G.bed -q 30 -Q 30 in.bam -o out.bcf Then: I can call snps from the bcf with at least two different commands: bcftools call -mV indels bcftools call -c -v I get two vastly different results wi ...
bcftools call snp written 8 days ago by cetin.m10 • updated 8 days ago by finswimmer8.8k
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Answer: A: Fst calculation between my own population and 1000 genome populations
... When I did something similar I used a python code which did not involve merging the files. ...
written 15 days ago by cetin.m10
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Beagle 4.1 imputation
... I am running Beagle 4.1 to impute SNPs in human WGS data. I ran chr 21 and it took 10 days. (with ~1M markers in the ref panel) That means the whole genome would take 2 years.. How do other people manage this? ...
imputation written 15 days ago by cetin.m10
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Comment: C: Choice of ref. Genomes
... Thanks!! Where can I find more information about how GRCh 38 was assembled? I did google but no find. ...
written 26 days ago by cetin.m10
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Choice of ref. Genomes
... The human reference genomes are just somebody's genome. What kind of errors and biases does this introduce? Can you please direct me to relevant websites or papers? ...
genome snp written 26 days ago by cetin.m10 • updated 26 days ago by igor7.2k
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Comment: C: Finding and changing a given position in hg19 ref fasta file
... Seems like exactly what I want! ...
written 27 days ago by cetin.m10
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Finding and changing a given position in hg19 ref fasta file
... I want to go to the hg19 reference fasta file and change say, position 727004 in chromosome 1 for a project. The file contains N's in the beginning. Where do I start counting to find position 727004? I am thinking of writing a python script to find the given positions and change them. Is there a ...
fasta reference hg19 written 27 days ago by cetin.m10
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Full genome phyloP scores from UCSC Browser
... Hi, I need phyloP scpres for the whole human genome. I was able to download 10M positions from http://genome.ucsc.edu/cgi-bin/hgTables using these instructions: group: Comparative Genomics track: Conservation table: your phyloP table of choice region: genome output format: data points How ...
database ucsc written 28 days ago by cetin.m10 • updated 28 days ago by cmdcolin1.0k

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