Question: Count the number of exons in a trasncript
0
gravatar for speycast
4 weeks ago by
speycast0
speycast0 wrote:

Hello,

I'd like to know how to count the number of exons in a given transcript using NCBI eutils? for example NM_020742.3.

thanks very much!

eutils transcript exon ncbi • 114 views
ADD COMMENTlink modified 4 weeks ago by genomax89k • written 4 weeks ago by speycast0
3
gravatar for genomax
4 weeks ago by
genomax89k
United States
genomax89k wrote:

Using Entrezdirect:

$ esearch -db nuccore -query "NM_020742.3" | efetch -format ft | grep - w "exon" | wc -l
       6

If you need starts and stops:

$ esearch -db nuccore -query "NM_020742.3" | efetch -format ft | grep -w "exon"
1   159 exon
160 936 exon
937 1089    exon
1090    1275    exon
1276    2065    exon
2066    5706    exon
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by genomax89k

Thanks so much genomax!!!!

ADD REPLYlink written 4 weeks ago by speycast0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1949 users visited in the last hour