To find total genes on favorable chromosome

To find total genes on favorable chromosome

2

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


genes


total

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Counting from GENCODE for the vM27 mouse reference:

wget http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M27/gencode.vM27.annotation.gtf.gz

#/ In R:
library(rtracklayer)
gtf <- rtracklayer::import("~/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 


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