Questions tagged [chromosomes]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1 vote
0 answers
13 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 ...
  • 1,733
0 votes
1 answer
37 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/...
  • 1,733
1 vote
1 answer
173 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....
3 votes
1 answer
55 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 ...
  • 1,733
2 votes
1 answer
70 views

How can I use pandas agg here to avoid iteration?

can anyone help me improve this pandas code? ...
1 vote
1 answer
32 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 ...
0 votes
3 answers
99 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 ...
  • 195
0 votes
1 answer
36 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.
2 votes
2 answers
34 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 ...
  • 2,234