Skip to content

vpandey-om/barseq-obilab

Folders and files

NameName
Last commit message
Last commit date

Latest commit

author
Vikash Pandey
Jan 26, 2023
4945700 · Jan 26, 2023

History

9 Commits
Feb 7, 2020
Jan 26, 2023
Feb 7, 2020
Feb 7, 2020
Feb 7, 2020
Jan 26, 2023
Jan 26, 2023
Feb 7, 2020
Jan 26, 2023
Feb 7, 2020
Feb 7, 2020
Feb 7, 2020
Feb 7, 2020
Feb 7, 2020
Feb 7, 2020
Feb 7, 2020
Jan 26, 2023
Feb 7, 2020
Feb 7, 2020
Feb 7, 2020
Feb 7, 2020
Jan 26, 2023

Repository files navigation

barseq-obilab

how to run

Install: Need some Library such as screed regex.

Step1 : python barseq.py -i data/sequence -b barcode_gene_file.csv -r testRes

arg1: barseq.py is script arg2 with -i: path for all fastq files containing folder arg3 with -b : barcode to gene mapping (for example see: barcode_gene_file.csv) arg4 with -r : user based result folder (testRes); you have to remove folder if script fails.

Step 2: remove all zero counts

python remove_zero_barseq_count.py testRes/barcode_counts_table.csv Result_after_removing_zero.csv

arg1: This file will be genrated after step 1. arg2: Desired file.

md5sum to test all fastq files are correctly downloaded.

for i in ls *md5;do md5sum -c $i; done

About

No description, website, or topics provided.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published