How to calculate the number of proteins present in each chromosomes?

Question

[Naresh]

Hi All, I have a bacterial species (Gimesia maria) which has 5865 protein sequence which is present in 14 chromosomes.

I would like to know how many proteins are present in each chromosomes.

Kindly help me.

Answer 1

[apa@stowers]

You need to specify what format your data are in. What to do depends entirely on what format your data are in.

I'll bet you have, or can get, a bed file of protein-coding genes? On the command line:

cut -f1 proteins.bed | sort -u | uniq -c

[WouterDeCoster]

I think you mean:

cut -f1 proteins.bed | sort | uniq -c

sort -u will already remove duplicates, there won't be much to count for uniq after that.

[apa@stowers]

You are right, and I consistently make that mistake on the actual command line too! Somehow "sort" always gets "-u", and then I have to go re-run my line... Ahh motor cortex...