20220107

Contents
  1. 1. Working directories
  2. 2. miRDB
  3. 3. samtools
  4. 4. wkhtmltopdf

Working directories

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E: Failed to fetch http://cn.archive.ubuntu.com/ubuntu/pool/universe/f/fonts-wqy-zenhei/fonts-wqy-zenhei_0.9.45-7ubuntu1_all.deb  Connection failed [IP: 91.189.91.39 80]
E: Failed to fetch http://cn.archive.ubuntu.com/ubuntu/pool/universe/f/fonts-wqy-microhei/fonts-wqy-microhei_0.2.0-beta-3_all.deb  Connection failed [IP: 91.189.91.39 80]
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?
# 
#########################################################################
# knitr powerpoint
cd /media/ht/ht_5T/Work/Conferences/Template

miRDB

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cd /media/ht/ht_5T/Database/miR_Base/miRDB
wget http://mirdb.org/download/miRDB_v6.0_prediction_result.txt.gz
wget http://mirdb.org/download/miRDB_v5.0_prediction_result.txt.gz
wget http://mirdb.org/download/MirTarget2_v4.0_prediction_result.txt.gz
wget http://mirdb.org/download/MirTarget2_v3.0_prediction_result.txt.gz
wget http://mirdb.org/download/MirTarget2_v2.0_prediction_result.txt.gz
wget http://mirdb.org/download/MirTarget2_v1.0_prediction_result.txt.gz

# 
lh `locate -b NC_001806_HSV-1.fas`
locate -b NC_001806_HSV-1.fas
# 
i=/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/DB/CG/NC_001806_HSV-1.fas
j=/media/ht/ht_5T/Work/Experiments/Primers/Primer_Design/20211117/LNG1/Original/NC_001806_HSV-1.fas
rm ${j}; ln -s ${i} ${j}
# 
j=/media/ht/ht_5T/Work/Experiments/Primers/Primer_Design/20211117/LNG2/Original/NC_001806_HSV-1.fas
rm ${j}; ln -s ${i} ${j}
# 
j=/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/DB/CG/20191025_1255/NC_001806_HSV-1.fas
rm ${j}; ln -s ${i} ${j}
# 
j=/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/DB/CG/20191025/NC_001806_HSV-1.fas
rm ${j}; ln -s ${i} ${j}
# 
cd /media/ht/ht_5T/Work/Projects/Exosome/RNA-Seq/20211203/Analysis/20220109

DB=/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/DB/MagicBLAST/HSV1_Ref
Query=/media/ht/ht_5T/Work/Projects/Exosome/RNA-Seq/20211203/Clean_Ctrl.fa
# 
Ref=
Seq=
Seq_Base=`basename ${Seq}`; Ref_Base=`basename ${Ref%.*}`; BAM=${Seq_Base%.*}_vs_`basename ${Ref_Base}`.bam
magicblast -query ${Seq} -subject ${Ref} -infmt fasta -outfmt sam | samtools view -bS -F 4 -> ${Seq_Base%.*}_vs_`basename ${Ref_Base}`_Mapped.bam # 序列中绝对禁止`-`，这类符号是经过MSA产生的
BAM=${Seq_Base%.*}_vs_`basename ${Ref_Base}`_Mapped.bam
samtools sort $BAM > "${BAM%.bam}.sort.bam"
samtools index "${BAM%.bam}.sort.bam"


Query=/media/ht/ht_5T/Work/Projects/Exosome/RNA-Seq/20211203/Clean_HSV1.fa

samtools

wkhtmltopdf

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i=https://wkhtmltopdf.org/
wkhtmltopdf ${i} `basename ${i}`.pdf
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{% if theme.mermaid.enable %} {% endif %}

tag:

    缺失模块。
    1、请确保node版本大于6.2
    2、在博客根目录（注意不是yilia根目录）执行以下命令：
    npm i hexo-generator-json-content --save

    3、在根目录_config.yml里添加配置： 

      jsonContent:
    meta: false
    pages: false
    posts:
      title: true
      date: true
      path: true
      text: false
      raw: false
      content: false
      slug: false
      updated: false
      comments: false
      link: false
      permalink: false
      excerpt: false
      categories: false
      tags: true

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