コンテンツに飛ぶ | ナビゲーションに飛ぶ

パーソナルツール

現在位置: ホーム / bisulfighter / bsf-call

bsf-call

NAME

Bisulfighter::bsf-call - a python script for short read mapping and methylated cytosine (mC) detection

SYNOPSIS

bsf-call [options] <reference_genome> <sequence_files>

OPTIONS

-c <integer>, --coverage=<integer>
Specify the threshold for valid read coverage for mC detection (default: 5).

-l <float>, --lover-bound=<float>
Specify the threshold for valid mC rate (default: 0.01).

-s <integer>
Specify the threshold for valid alignment score (default: 150)

-m <float>
Specify the threshold for filtering mis-mapping probability (default: 0.01)

-p <integer>, --multi-thread=<integer>
Specify the number of threads (default: 1)

-o <filename>
Specify the filename for the output (default: stdout)

--last=<opt,opt,...>
Specify options passed to lastal command.
"-s" and "-Q" options are automatically specified by bsf-call.

-W <path>
Specify the working directory (default: ./bsf-call_work ).

--work-wuto
Let bsf-call determine the working directory automatically.
-W option cancels this option.

REFERENCE GENOME

Specify the filename for the reference genome, which is a multi-fasta file.
Example: hg19/hg19.fa

SEQUENCE FILES

Specify a list of sequence files to be mapped.
Supports FASTQ, SRA and FASTA.
File formats are identified with extension of input filenames.
Please make sure bsf-call assumes all input reads are forward-stranded no matter if they are single or paired.

Example:

1) multiple single reads

single-sample1.fastq single-sample2.fastq 

2) multiple paired reads

paired-sample1-1.fastq,paired-sample1-2.fastq paired-sample2-1.fastq,paired-sample2-2.fastq 

3) mixture of single and paired reads

single-sample1.fastq paired-sample1-1.fastq,paired-sample1-2.fastq

EXAMPLE

bsf-call -c 10 -m 0.1 -s 250 -o experiment.txt --last=-d108,-e120,-i1 -W mywork hg19/hg19.fa paired-sample1-1.fastq,paired-sample1-2.fastq single-sample1.fasta

OUTPUT FORMAT

bsf-call outputs six column tab-delimited text file.

Col.Description
1 chromosome label (e.g. chr1)
2 genomic position (0-based)
3 strand (+,-)
4 mC context (CG, CHG, CHH)
5 mC rate (float)
6 read coverage

Example:

chr1    45241    +    CG    0.72    19
chr2    71345    +    CHG   0.04    21
chr10   71345    -    CHH   0.07    5
chrX    52123    +    CG    0.21    21

AUTHOR

Junko Tsuji
Toutai Mituyama

LICENSE

Creative Commons License
Bisulfighter by National Institute of Advanced Industrial Science and Technology (AIST) is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.