Analysis of barseq data.
Project description
barseq
Python package for analyzing barseq data.
Installation
pip install git+https://github.com/mjmlab/barseq.git@master
Usage
barseq -i <directory of sequencing reads> -b <barcode file> -e <experiment name>
-i
/ --input
- Directory with Illumina reads in either fastq or fastq.gz.
-b
/ --barcodes
- CSV file with barcode and correspondent gene names.
-e
/ --experiment
- Name of experiment, it is used for creating results folder.
Files Needed
Directory of Illumina reads [-i
] for analyzing. Can be either fastq or fastq.gz format
@M06026:87:000000000-D69HY:1:1102:15909:1336 1:N:0:TGACCA
CTCTAGAAAGTATAGGAACTTCAGGGCCATTTATATACCTTCCACTCTTCAACCGTGTCTTGACTTGACCTGGATGTCTCTACTGCTGTCATGCTACGTAGCTCATGCTACGTCGATCTAGTCGATGCATGCTAGCTGATCGACTCTCTTC
+
A#>>>3AA2DD>FBFGBFBFBFDDFGGAAEEEHDHFFFDDDBDGDFDDDDDADFGFFDDBFFEBFD5DFEEBBADABFGFGBBFGDD5BF3F43B3F1/11B144BGEBF@BBFB0B0BBFBBBBBBBB?E/FGFBB?/???B???/?FGG
Barcode file [-b
] with gene names. Needs to be in CSV format.
Barcode,Gene
ATGAAGACTGTTGCCGTA,WT
CACGACGCCCTCCGCGGA,gene1
ACTATTACGCAAAATAAT,gene2
ATGGAAGATATTATTATT,gene3
CCTCTCCAACCGGGTCTG,gene4
CCCGGTCGCCTAGCCCCG,gene5
GGCCCCCCGCCCGTCCCC,gene6
GGATCACTGCTAGCGTAT,gene7
CCTGCAGCAGCGGCCCGC,gene8
ACACATGCAGACATAGAG,gene9
CGCGCCATCCGCCGCCCA,gene10
AATATTCAGATGGGACGT,gene11
Output
results/
directory
- _results.csv: barcode counts found in each sequence file.
Gene | Barcode | Sample 1 | Sample 2 | Sample 3 | ... |
---|---|---|---|---|---|
gene1 | ATGAAGACTGTTGCCGTA |
500 | 5 | 7 | ... |
gene2 | CACGACGCCCTCCGCGGA |
12 | 13 | 19 | ... |
gene3 | ACTATTACGCAAAATAAT |
13 | 11 | 10 | ... |
_other | _other | 28 | 40 | 29 | ... |
Barseq Workflow
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