Questions tagged [chromosomes]

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1answer
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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
vote
1answer
64 views

How can I use pandas agg here to avoid iteration?

can anyone help me improve this pandas code? ...
1
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1answer
26 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
3answers
89 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 ...
0
votes
1answer
31 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
2answers
33 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 ...