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古郡 まさき edited this page Mar 12, 2024
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Welcome to the Pore-C-analysis wiki!
This responsiblity was used to store PORE-C analysis methods.
I recommand Wf-pore-C(https://github.com/epi2me-labs/wf-pore-c) for align and annotate bam files. Notice that it requires docker.
本人修改过一个优化过运行速度的流程,可以通过以下命令下载:
wget https://github.com/gotouerina/Pore-C-analysis/releases/download/v1.0/modify-wf-pore-c.tar.gz
tar -xf https://github.com/gotouerina/Pore-C-analysis/releases/download/v1.0/modify-wf-pore-c.tar.gz
注意,该流程基于nextflow,需要dcoker支持运行。
/path/to/nextflow run /path/to/wf-pore-c \
--fastq $fq.gz --ref $fasta --cutter NlaIII -c increase_memory.config \
--threads 60 --paired_end_minimum_distance 100 --paired_end_maximum_distance 200 \
--chunk_size 10000 --paired_end
断点重连:添加--resume参数。断电关机,重连后可用。
目前只跑通了yahs(https://github.com/c-zhou/yahs), 1.1版本 (1.2版本使用bam文件会报错,作者没修)
samtools faidx $fasta
/path/to/yahs -e CATG Bathyergus.fasta null.ns.bam (e接酶切位点,不同酶不同)
/path/to/juicer pre -a -o out_JBAT yahs.out.bin yahs.out_scaffolds_final.agp $i.fasta.fai
##这一步会提示下一步命令行是什么,echo 后面的会不一样
java -Xmx300G -jar juicer_tools_1.22.01.jar pre --threads 30 out_JBAT.txt out_JBAT.hic <(echo "assembly 1382974809")
将.assemble文件和.hic导入juicebox纠错即可
调整挂载结果
/yahs-1.1/juicer post -o out_JBAT out_JBAT.review.assembly out_JBAT.liftover.agp $fasta
/yahs-1.1/agp_to_fasta out_JBAT.liftover.agp $fasta > $fasta.v1.chr.fasta
python juicer_assembly2agp_fa.py out_JBAT.review.assembly $fasta.chr.v1.fasta $fasta.chr.v2.fasta 28 0 ##28是染色体数量