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Questions tagged [chromosomes]

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Can I interpret 15x coverage area as a part of one strand is missing?

This is a BAM file from a 30x coverage Nebula Genomics test opened with IGV. I found an area (1:30169255-30169600) where the coverage is less than 15x. Can I interpret it as a part of one strand of ...
if0615's user avatar
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0 votes
1 answer
136 views

Why are genetic algorithm chromosomes represented using 8 bit binary?

I am learning about genetic algorithms. Why chromosomes are represented using 8 bit binary. This arose when I apply crossover techniques to the bits. Please help me to find the answer.Thanks in ...
Julie's user avatar
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1 vote
0 answers
24 views

Handling of sex chromosomes in male when computing CNV copy ratio

Reading from CNVkit documentation, Mathworks documentation, Bionano documentation, for CNV calling, it seems that the common practice for array is to compute the linear copy ratio by normalizing ...
gc5's user avatar
  • 1,813
0 votes
1 answer
298 views

Extract chromosome arms' coordinates for specific reference

I would like to get chromosome arms' coordinates for genome reference hs37d5 (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/...
gc5's user avatar
  • 1,813
1 vote
1 answer
612 views

imputed dosage values for vcf files

I have one more question related to genotype file. I submitted the job in michigan imputation server. and my imputed dosage for chr 22 file is: 22 16050435 22:16050435:T:C T C . PASS AF=0.00098;MAF=0....
Rhea Bedi's user avatar
3 votes
1 answer
113 views

Defining a bedfile for chromosome X without pseudo-autosomal regions

I would like to define a bedfile for chromosome X, to target only basepairs outside of pseudo-autosomal regions (and going forward other regions, too). First, I wasn't able to find an already prepared ...
gc5's user avatar
  • 1,813
2 votes
1 answer
75 views

How can I use pandas agg here to avoid iteration?

can anyone help me improve this pandas code? ...
Liam McIntyre's user avatar
2 votes
1 answer
44 views

Get a single number representing the contact probability between a pair of genomic loci using HiC data

Hello to the experts in analyzing chromosome structure data in HiC format, I have a very basic question. I have a HiC file (specifics are mentioned below), using which I would like to obtain contact ...
user345394's user avatar
0 votes
3 answers
126 views

Gene information from chromosome location

I have a file that contains species name, chromosome, start and end locations like the following format hg19,chr8,77778733,77779026. I would like to know some ...
SBDK8219's user avatar
  • 195
0 votes
1 answer
58 views

General question: How to assign my SNP (Wheat, Illumina 15K) to specific chromosomes?

I have 2000 lines of wheat genotyped with a 15K illumina chip. I also have the name of the SNPs. I would like to know how could I find out which SNPs are in each chromosomes.
marb_021's user avatar
2 votes
2 answers
41 views

fixing chromosome with new contig

I want to fix a chromosome of around 50-100Mb (chr.fasta) for a region that is missing a few kilobases of data. I have the missing sequence with a window upstream ...
719016's user avatar
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