parris：利用iso-seq分析和注释圆形rna
parris的Python项目详细描述
H1> PARRIS：用Iso Seq 分析和注释循环RNA
开始
安装
^ STR 1 } $ PARRIS<<强>是用^ {CD1>}编写的，请使用^ {CD2>}来安装^ {STR 1 } $ PARRIS：
pip install parris
或，您可以按照指令安装^ {STR 1 } $PARRIS从源：
git clone https://github.com/yangao07/PARRIS.git
cd PARRIS
python setup.py install # install main package
pip install -r requirements.txt # install dependencies
另外，请确保系统中安装了^{
命令示例1：
parris -t 8 long_circRNA.fa reference.fa gene_anno.gtf circRNA.bed output_folder
命令示例2:
parris -t 8 long_circRNA.fa reference.fa gene_anno.gtf circRNA.bed output_folder \
--short-read short_read.fa \
--Alu ./anno/hg19/alu.bed \
--all-repeat ./anno/hg19/all_repeat.bed
详细参数：
parris -h
usage: parris [-h] [-v] [-t THREADS] [--short-read short.fa] [--lordec LORDEC]
[--kmer KMER] [--solid SOLID] [--trf TRF] [--match MATCH]
[--mismatch MISMATCH] [--indel INDEL] [--match-frac MATCH_FRAC]
[--indel-frac INDEL_FRAC] [--min-score MIN_SCORE]
[--max-period MAX_PERIOD] [--fxtools FXTOOLS]
[--min-len MIN_LEN] [--min-copy MIN_COPY] [--min-frac MIN_FRAC]
[--minimap MINIMAP] [-f] [--high-max-ratio HIGH_MAX_RATIO]
[--high-min-ratio HIGH_MIN_RATIO]
[--high-iden-ratio HIGH_IDEN_RATIO]
[--high-repeat-ratio HIGH_REPEAT_RATIO]
[--low-repeat-ratio LOW_REPEAT_RATIO] [--Alu ALU]
[--flank-len FLANK_LEN] [--all-repeat ALL_REPEAT] [-s SITE_DIS]
[-S END_DIS]
long.fa ref.fa anno.gtf circRNA.bed/gtf output
PARRIS: Profiling and Annotating ciRcular RNA with Iso-Seq
positional arguments:
long.fa Long read data generated from long-read circRNA
sequencing technique.
ref.fa Reference genome sequence file.
anno.gtf Whole gene annotation file in GTF format.
circRNA.bed/gtf circRNA annotation file in BED12 or GTF format.
output Output directory for final result and temporary files.
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
General options:
-t THREADS, --threads THREADS
Number of thread to use. (default: 8)
Hybrid error-correction with short-read data (LoRDEC):
--short-read short.fa
Short-read data for error correction. Use ',' to
connect multiple or paired-end short read data.
(default: )
--lordec LORDEC Path to lordec-correct. (default: lordec-correct)
--kmer KMER k-mer size. (default: 21)
--solid SOLID Solid k-mer abundance threshold. (default: 3)
Detecting tandem-repeat with TRF(Tandem Repeat Finder):
--trf TRF Path to trf program. (default: trf409.legacylinux64)
--match MATCH Match score. (default: 2)
--mismatch MISMATCH Mismatch penalty. (default: 7)
--indel INDEL Indel penalty. (default: 7)
--match-frac MATCH_FRAC
Match probability. (default: 80)
--indel-frac INDEL_FRAC
Indel probability. (default: 10)
--min-score MIN_SCORE
Minimum alignment score to report. (default: 100)
--max-period MAX_PERIOD
Maximum period size to report. (default: 2000)
Extracting and aligning consensus sequence to genome (minimap2):
--fxtools FXTOOLS Path to fxtools. (default: fxtools)
--min-len MIN_LEN Minimum consensus length to keep. (default: 30)
--min-copy MIN_COPY Minimum copy number of consensus to keep. (default:
2.0)
--min-frac MIN_FRAC Minimum fraction of original long read to keep.
(default: 0.0)
--minimap MINIMAP Path to minimap2. (default: minimap2)
-f, --do-classify Classify circRNA alignment into high-quality and low-
quality. (default: False)
--high-max-ratio HIGH_MAX_RATIO
Maximum mappedLen / consLen ratio for high-quality
alignment. (default: 1.1)
--high-min-ratio HIGH_MIN_RATIO
Minimum mappedLen /consLen ratio for high-quality
alignment. (default: 0.9)
--high-iden-ratio HIGH_IDEN_RATIO
Minimum identicalBases/ consLen ratio for high-quality
alignment. (default: 0.75)
--high-repeat-ratio HIGH_REPEAT_RATIO
Maximum mappedLen / consLen ratio for high-quality
self-tandem consensus. (default: 0.6)
--low-repeat-ratio LOW_REPEAT_RATIO
Minimum mappedLen / consLen ratio for low-quality
self-tandem alignment. (default: 1.9)
Evaluating circRNA with annotation:
--Alu ALU Alu repetitive element annotation in BED format.
(default: )
--flank-len FLANK_LEN
Length of upstream and downstream flanking sequence to
search for Alu. (default: 500)
--all-repeat ALL_REPEAT
All repetitive element annotation in BED format.
(default: )
-s SITE_DIS, --site-dis SITE_DIS
Allowed distance between circRNA internal-splice-site
and annoated splice-site. (default: 0)
-S END_DIS, --end-dis END_DIS
Allowed distance between circRNA back-splice-site and
annoated splice-site. (default: 10)
变更日志（v1.5.9）
- 修复搜索已知拼接接头时出现的错误。
- 使用已知和规范的内部拼接链信息来指导反向拼接连接的搜索。
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