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Count the number of exons in a trasncript

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!

ncbi exon transcript eutils
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updated by GenoMax GenoMax • written by speycast • speycast

1 answer

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
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written by GenoMax GenoMax

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