Published July 14, 2022
| Version v1
Software
Open
Python scripts to access ArLV1 reads in SRAs of Arabidopsis accessions
Contributors
Description
Protocol Findblast script
Intral python 3.6: https://www.python.org/downloads/
Download ncbi sratoolkit: https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/
windows: https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.6-1/
put a fasta file with the sequence that you would like to search in the sratoolkit folder where blastn_vdb is located (=Bin folder)
make sure that Findblast.py is in the folder where python is located
make a tekst file in which the accessions are written and save these in the same python folder as Findblast.py. (my laptop could take about 100 accessions per file)
Open Findblast.py
Files
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