Bioinformatics Tools

ENVS

• create env file
• WES environment.yml file
• RNA environment.yml file
• scRNA(not done) environment.yml file

Download and processing

• Method to download bam file from TCGA & SRA (not done)
• bam to fastq & QC

WES, RNA, scRNA shell

• Executable files, from bam to the final step (QC included in Download and Processing)

Other

• 不知道是啥

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TODO

Download and preprocessing

• download bam from GDC
• select samples by sample sheet
• download fastq from SRA
• env file
• bam → fastq sh
• fastqc & multiqc
• trim fastq (Trimmomatic)

WES

• fastq → bam (BWA-mem)
• variants calling
  • muse
  • mutect2
  • varscan
  • pindel
• vcf merge python
  • preprocessing
  • merge
  • status table
• vep python
• vep vcf → maf
• maf → maftool format maf

RNA-seq

• env file
• make indices (RSEM, kallisto)
• fastq → abundance table (kallisto, K-mer base pseudo alignment method)
• fastq → bam (STAR)
• bam → count matrix (RSEM)
• visualize count matrix & distribution

Methylation

• preprocessing
• DMP
• DMR

Others

• config
• template
• send message python script (Telegram)