Deleted:Difficulty returning appropriate info. with esearch and/or efetch
0
0
Entering edit mode
7 weeks ago
Vincent Laufer ★ 2.4k

Hello,

A few days ago I asked some questions regarding how to find associated genomic data easily.

GenoMax recommended efetch and esearch, as can be seen here: Extract nucleotide sequence from a RefSeq Transcript ID

Since this time I have been using these tools; for some reason, though, I am hitting a snag when pulling genetic variants within a given gene ... I have a couple working versions; for instance, e

esearch -db snp -query "FGFR2" | efetch -format docsum

gives me approximately the right information, but no rsIDs are provided. Other queries also get me close, but for instance without variant annotation information (i.e. this results in a missense).

is there a simple way to emend the above query so it gives me rsID, chr, pos, functional info, and (ideally) more?

TYVM

esearch dbsnp efetch • 113 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 1593 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6