CPDseq data analysis
Project description
CPDSeqer
This package is used to do CPD sequence data analysis.
Prerequisites
Install tabix
apt-get install -y tabix
Installation
Install python main package
pip install git+git://github.com/shengqh/cpdseqer.git
Usage
Demultiplex fastq file
usage: cpdseqer demultiplex [-h] -i [INPUT] -o [OUTPUT] -b [BARCODEFILE]
optional arguments:
-h, --help show this help message and exit
-i [INPUT], --input [INPUT]
Input fastq gzipped file
-o [OUTPUT], --output [OUTPUT]
Output folder
-b [BARCODEFILE], --barcodeFile [BARCODEFILE]
Tab-delimited file, first column is barcode, second
column is sample name
for example:
cpdseqer demultiplex -i sample.fastq.gz -o . -b barcode.txt
Example of barcode.txt, columns are separated by tab
ATCGCGAT Control
GAACTGAT UV
Align reads to genome using bowtie2
bowtie2 -p 8 -x hg38/bowtie2_index_2.3.5.1/GRCh38.p12.genome -U Control.fastq.gz \
--sam-RG ID:Control --sam-RG LB:Control --sam-RG SM:Control --sam-RG PL:ILLUMINA \
-S Control.sam 2> Control.log
samtools view -Shu -F 256 Control.sam | samtools sort -o Control.bam -T Control -
samtools index Control.bam
rm Control.sam
You can download hg38 bowtie2 index files:
mkdir hg38
cd hg38
wget https://cqsweb.app.vumc.org/download1/cpdseqer/hg38_bowtie2.tar.gz
tar -xzvf hg38_bowtie2.tar.gz
cd ..
Extract dinucleotide from bam file
usage: cpdseqer bam2dinucleotide [-h] -i [INPUT] -g [GENOME_SEQ_FILE]
[-q [MAPPING_QUALITY]] -o [OUTPUT]
optional arguments:
-h, --help show this help message and exit
-i [INPUT], --input [INPUT]
Input BAM file
-g [GENOME_SEQ_FILE], --genome_seq_file [GENOME_SEQ_FILE]
Input genome seq file
-q [MAPPING_QUALITY], --mapping_quality [MAPPING_QUALITY]
Minimum mapping quality of read (default 20)
-o [OUTPUT], --output [OUTPUT]
Output file name
for example:
cpdseqer bam2dinucleotide \
-i Control.bam \
-g hg38/bowtie2_index_2.3.4.1/GRCh38.p12.genome.fa \
-o Control.dinucleotide.bed.bgz
You can download bam files:
wget https://cqsweb.app.vumc.org/download1/cpdseqer/UV.bam
wget https://cqsweb.app.vumc.org/download1/cpdseqer/UV.bam.bai
wget https://cqsweb.app.vumc.org/download1/cpdseqer/Control.bam
wget https://cqsweb.app.vumc.org/download1/cpdseqer/Control.bam.bai
Get statistic based on bed file
usage: cpdseqer statistic [-h] -i [INPUT] -c [COORDINATE_LIST_FILE] [-s]
[--category_index CATEGORY_INDEX] [--add_chr] -o
[OUTPUT]
optional arguments:
-h, --help show this help message and exit
-i [INPUT], --input [INPUT]
Input dinucleotide list file, first column is file
location, second column is file name
-c [COORDINATE_LIST_FILE], --coordinate_list_file [COORDINATE_LIST_FILE]
Input coordinate list file, first column is file
location, second column is file name
-s, --space Use space rather than tab in coordinate files
--category_index CATEGORY_INDEX
Zero-based category column index in coordinate file
--add_chr Add chr in chromosome name in coordinate file
-o [OUTPUT], --output [OUTPUT]
Output file name
for example:
cpdseqer statistic --category_index 3 \
-i cpd__fileList1.list \
-c cpd__fileList2.list \
-o cpd.dinucleotide.statistic.tsv
cpd__fileList1.list (separated by tab)
Control.dinucleotide.bed.bgz Control
UV.dinucleotide.bed.bgz UV
cpd__fileList2.list (separated by tab)
hg38_promoter.bed Promoter
hg38_tf.bed TFBinding
You can download example files as following scripts. The hg38_promoter.bed contains three columns only. So, Promoter (from cpd__fileList2.list definition) will be used as category name for all entries in the hg38_promoter.bed. The hg38_tf.bed contians four columns. The forth column in hg38_tf.bed indicates TF name which will be used as category name (--category_index 3) instead of TFBinding.
wget https://cqsweb.app.vumc.org/download1/cpdseqer/UV.dinucleotide.bed.bgz
wget https://cqsweb.app.vumc.org/download1/cpdseqer/UV.dinucleotide.bed.bgz.tbi
wget https://cqsweb.app.vumc.org/download1/cpdseqer/Control.dinucleotide.bed.bgz
wget https://cqsweb.app.vumc.org/download1/cpdseqer/Control.dinucleotide.bed.bgz.tbi
wget https://cqsweb.app.vumc.org/download1/cpdseqer/cpd__fileList1.list
wget https://cqsweb.app.vumc.org/download1/cpdseqer/cpd__fileList2.list
wget https://github.com/shengqh/cpdseqer/raw/master/data/hg38_promoter.bed
wget https://github.com/shengqh/cpdseqer/raw/master/data/hg38_tf.bed
Running cpdseqer using singularity
We also build docker container for cpdseqer which can be used by singularity.
Running directly
singularity exec -e docker://shengqh/cpdseqer bowtie2 -h
singularity exec -e docker://shengqh/cpdseqer cpdseqer -h
Convert docker image to singularity image first
singularity build cpdseqer.simg docker://shengqh/cpdseqer
singularity exec -e cpdseqer.simg bowtie2 -h
singularity exec -e cpdseqer.simg cpdseqer -h
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