To find total genes on favorable chromosome

Question

[Jraha1989]

How can I find how many genes exist on each chromosome?

[Jraha1989]

Thanks, guys. But the count on NCBI is completely different from your solution for the proposed chromosome.

[GenoMax]

Can you specify for which genome?

ATpoint solution is for Mouse genome. My answer points you to the web page of official bodies that assign human/mouse gene names. If they have not assigned a gene name for a particular gene then it is only a prediction/suggestion.

[Jraha1989]

human, chr4.

[ATpoint]

Just replace the mouse gtf with the human one from gencode, same code, will take < 1' to complete.

Answer 1

[ATpoint]

Counting from GENCODE for the vM27 mouse reference:

#/ In R:
library(rtracklayer)
gtf <- rtracklayer::import("http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M27/gencode.vM27.annotation.gtf.gz")
table(as.character(seqnames(gtf[gtf$type=="gene"])))

chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19  chr2  chr3  chr4  chr5  chr6  chr7  chr8  chr9  chrM  chrX  chrY 
 3445  2622  2999  2474  2502  2509  1852  1602  2320  1399  1394  3794  2884  2861  3251  3129  4713  2535  2845    37  2623  1569 

Answer 2

[GenoMax]

For Human genes you can find this information via a web page here.

For mouse if you prefer a web based option.