How to pull metadata from SRA based on Run id?

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2.1 years ago

Sidra • 0

I have a lot of SRR ids. I got this code line -->

esearch \
  -db sra \
  -query SRR1751234 | \
efetch \
  -format runinfo \
  -mode xml | \
xtract \
  -pattern SraRunInfo \
  -element BioProject BioSample Modelesearch \
  -db sra \
  -query SRR1751234 | \
efetch \
  -format runinfo \
  -mode xml | \
xtract \
  -pattern SraRunInfo \
  -element BioProject BioSample Model

Output like this -->>

PRJNA186035 SAMN02345261 Illumina MiSeq

But I also need collection date,country. Can anyone help me? I need command line which can read my srr ids file and give the summary of that attributes.

metadata sra • 658 views

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 2.1 years ago by Sidra • 0

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XMLStarlet is the tool you are looking for.

ADD REPLY • link 2.1 years ago by Matthias Zepper 5.0k

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Please don't get used to opening multiple questions on the same topic. Keep it focused in a single one: sra data

ADD REPLY • link 2.1 years ago by ATpoint 85k

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