Question: How to calculate the number of proteins present in each chromosomes?
0
gravatar for Naresh
7 days ago by
Naresh50
Korea, Republic Of
Naresh50 wrote:

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.

R genome • 114 views
ADD COMMENTlink modified 7 days ago by apa@stowers320 • written 7 days ago by Naresh50
0
gravatar for apa@stowers
7 days ago by
apa@stowers320
Kansas City
apa@stowers320 wrote:

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

ADD COMMENTlink modified 7 days ago • written 7 days ago by apa@stowers320

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.

ADD REPLYlink written 7 days ago by WouterDeCoster11k

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...

ADD REPLYlink written 7 days ago by apa@stowers320
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