Bioinformatics Scripts

Curated SciBerg command-line and bioinformatics scripting tutorials.

• Calculate Raw Read Counts with eXpress and RSEM
• Converting GTF Files into BED Files
• Extracting Promoter and TSS Sequences from Genome FASTAs
• Extracting Specific Sequences from FASTA Files
• Manipulation with FASTA and FASTQ Files in Linux
• Manipulations with SAM Files
• Preparing FASTA References for Main RNA Classes
• Primary Analysis of FASTQ Files
• Reads Alignment with Bowtie, Bowtie2, BWA, HISAT2 and STAR
• Removing Duplicated Sequences from FASTA Files
• Trimming and Filtering of NGS Reads