pbb-drylab

dry lab methods used by @PuckerLab

WARNING: Some of this content is not publicly available. If you are not a member of the PuckerLab, you might not be able to use it.

Introduction

All scripts are available in /grp/pbb/scripts. Additional tools can be found in /grp/pbb/tools.

Scripts (developed by group)

automatic_SRA_download.py

BWA_MEM_wrapper.py

collect_best_BLAST_hits.py

construct_DESeq2_input.py (requires modification!)

DGE_analysis.R

extract_myb_domain.py

filter_RNAseq_samples.py

get_DEGs_from_DESeq2_output.py

kallisto_pipeline.py

mask_monophyly_bp.py

merge_kallisto_output.py

reads2counts2.py

rename_FASTA_seqs.py

tree.py

tree2.py

Standard tools (developed by others)

A large number of tools is installed globally thus you just have to type the name of your tool into the terminal to use it.

FastQC / MultiQC

BWA-MEM

FastTree

IGV

Picard-tools

RAxML

Samtools

SRAtoolkit (fastq-dump)

STAR

Trimmomatic

Trinity

Single cell RNA-seq (scRNA-seq)

CellRanger for quantification of reads.

There is an excellent book about the following analysis: Orchestrating Single Cell Analysis with Bioconductor