From 44fec3d53dbd961c3a6598c57bd39f9fc9358171 Mon Sep 17 00:00:00 2001 From: Lan Hui Date: Fri, 24 Oct 2025 14:17:53 +0800 Subject: Information on how to tell whether a run is RNA-seq or not --- Code/download_ena_experiment_records.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) (limited to 'Code') diff --git a/Code/download_ena_experiment_records.py b/Code/download_ena_experiment_records.py index 11bfc70..d96071f 100644 --- a/Code/download_ena_experiment_records.py +++ b/Code/download_ena_experiment_records.py @@ -5,10 +5,15 @@ # # Note: # (1) The experiment accession IDs are stored in ../Data/information/experiment_ids_lacking_strategy_or_source.txt -# (2) Given an experiment's accession SRX6711770, we can get its full information from the following link -# https://www.ebi.ac.uk/ena/browser/api/xml/SRX6711770 +# (2) Given an experiment's accession SRX6711770, we can get its full information (e.g., whether it is RNA-seq) from the following link https://www.ebi.ac.uk/ena/browser/api/xml/SRX6711770 +# (3) Each run is associated with an experiment. Therefore, we can find whether the run is RNA-seq by first finding its associated experiment accession, then from the experiment +# accession finding its library strategy and library source. +# For example, for run SRR23878410, from https://www.ebi.ac.uk/ena/browser/api/xml/SRR23878410 we know that its associated experiment accession is SRX19690458, and +# from https://www.ebi.ac.uk/ena/browser/api/xml/SRX19690458 we know that its library strategy is RNA-seq and its library source is TRANSCRIPTOMIC. # -# 2025-10-23 +# Last modified by Hui on: +# 2025-10-23 +# 2025-10-24 import urllib.request import os, time, glob -- cgit v1.2.1