From d6a88527737105bedd9d350a4f8cfb2f06c09db2 Mon Sep 17 00:00:00 2001 From: tony006469 Date: Mon, 15 Oct 2018 09:35:07 -0400 Subject: [PATCH] add download_sra_metadata.py --- README.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 41ddd5a..9bb15c6 100644 --- a/README.md +++ b/README.md @@ -22,6 +22,16 @@ A RNA-Seq annotation pipeline based on [SRA Toolkit](https://github.com/ncbi/sra ## Usage ``` shell + +download_sra_metadata.py [-t TAXID] [-o [OUTPUT]] + +Use pipeline to download the sra metadata,the output file will be used for the input file of RNAseq_annotate.py. + +optional arguments: + -t TAXID, --taxid TAXID find all RNA SRA files for a given taxid + -o [OUTPUT], --output [OUTOUT] directory and name of output folder at, if not specified, use current folder + + RNAseq_annotate.py [-h] [-i INPUT] [-g GENOME] [-n [NAME]] [-o [OUTDIR]] [-d] @@ -45,7 +55,7 @@ optional arguments: ``` ## Example - +- `download_sra_metadata.py -t 1049336 -o 1049336.tsv` - `wget "https://i5k.nal.usda.gov/data/Arthropoda/ephdan-(Ephemera_danica)/Current%20Genome%20Assembly/1.Genome%20Assembly/BCM-After-Atlas/Scaffolds/Edan07162013.scaffolds.fa.gz"` - `RNAseq_annotate.py -i ./example/1049336.tsv -g ./Edan07162013.scaffolds.fa.gz -d`