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Welcome to the HamidLab Wiki!

This wiki is a central repository of standard operating procedures (SOPs) for our lab, and it is a great way to stay up-to-date on the latest softwares and analyses.

This wiki is open to all lab members including internship students, and we encourage you to contribute to routinely used codes and protocols. If you have any questions or suggestions, please don't hesitate to drop a chat on our lab's Slack channel!

On the right of this wiki, you will find the different sections/pages. Toggle the drop-down list to reveal the subsections of each page. Hyperlinks to frequently used protocols can be found in the right below the Pages list.

Here is a brief overview of the different sections of the wiki:

• HamidLab routines: How do I access the workstation? How do I create Quarto reports using lab templates?

• Retrieving data: How do I download data from Sequence Read Archive (SRA) or commonly used File Transfer Protocol (FTP) servers?

• Nextflow pipelines: How do I run NextFlow's pipelines from the workstation?

• Bulk-RNAseq: How do I perform quality control (QC) on short-read sequences? How do I align and quantify transcript/gene expression? How do I analyse RNA-seq data for alternative splicing?

• Single-cell RNAseq: How do I align 10X FASTQ files? How do I process gene-expression data? How do I integrate data?

• BASH commands:

• R analyses: How do I perform differential expression analyses? How do I cluster features? How do I create plots?

• suite2p: How do I set up the environment for running suite2p? How do I set the input parameters for suite2p? How do I read the output files?

• Software and packages: What are the installing tools and software available for me to use? How do I download and store other source codes?

Got new ideas for a wiki page? Leave them below!

• Long-read sequencing