Python package for analyzing barseq data.
pip install git+https://github.com/mjmlab/barseq.git@masterbarseq -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.
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
- _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 | ... |
