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1. data-sandbox data-sandbox Public

   A collection of exploratory data science and machine learning projects across bioinformatics, cheminformatics, and clinical data visualization.

   Jupyter Notebook

2. NGS-Methods-Development NGS-Methods-Development Public

   A repository for next-generation sequencing (NGS) methods development and benchmarking projects. This repository contains analyses comparing different library preparation approaches and custom prot…

   R

3. Tools Tools Public

   Collection of bioinformatics tools for various NGS (Next-Generation Sequencing) data processing tasks. (Python, R, PERL and Shell)

   Perl

4. Workflows Workflows Public

   Two bioinformatics workflow pipelines for NGS data processing: Snakemake workflow for demultiplexing and quality control of raw sequencing data, and Nextflow pipeline for single-cell RNA sequencing…

5. How to demultiplex based on I5 index... How to demultiplex based on I5 index and have I7 index as a separate read

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   If you want the I7 indexes on a standalone FastQ file (R2 file will have the I7 indexes), then 

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       Step 1. first modify your RunInfo.xml file by changing  

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           <Read Number="2" NumCycles="8" IsIndexedRead="Y" />  

6. CRISPR Screen - NGS FASTQ to Count File CRISPR Screen - NGS FASTQ to Count File

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   Step 1.3, Step 2.1 to 2.3 and Step 3.1 can be done for a given fastq file and reference fasta using the following shell script: https://github.com/sumeetg23/Tools/blob/master/Shell/CRISPR-Generate-Count.sh

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   Step 3.2 script is available here: https://github.com/sumeetg23/Tools/blob/master/R/CRISPR_CountSummary_v1.2.R

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   # Step 1: Generate Bowtie Index