RC
Calculate Raw Read Counts with eXpress and RSEM
Generate raw transcript or gene-level counts from RNA-seq alignments using eXpress and RSEM workflows.
RNA-seqQuantificationCounts
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Bioinformatics Scripts
Practical command-line workflows for everyday bioinformatics.
A curated SciBerg collection of practical command-line guides for FASTA, FASTQ, SAM, gene annotations, read alignment, RNA quantification and other recurring analysis tasks.
Scripts
Reusable workflows for common analysis tasks.
Open a guide for the commands, rationale and practical steps behind each workflow.
GB
Converting GTF Files into BED Files
Convert GTF gene annotations into BED coordinates for downstream genomic analysis and interval-based tools.
GTFBEDAnnotation
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TS
Extracting Promoter and TSS Sequences from Genome FASTAs
Extract promoter and transcription-start-site sequences from a reference genome using genomic coordinates.
FASTAPromotersTSS
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FS
Extracting Specific Sequences from FASTA Files
Retrieve selected records or sequence regions from FASTA files with practical command-line approaches.
FASTASequence extractionLinux
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FQ
Manipulation with FASTA and FASTQ Files in Linux
Common Linux operations for inspecting, filtering, transforming and reorganizing FASTA and FASTQ data.
FASTAFASTQShell
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SA
Manipulations with SAM Files
Practical commands for filtering, inspecting and processing SAM alignment files in sequencing workflows.
SAMAlignmentLinux
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RF
Preparing FASTA References for Main RNA Classes
Build curated FASTA references for major RNA classes for mapping, classification and sequential-analysis workflows.
RNAFASTAReference
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QA
Primary Analysis of FASTQ Files
A practical route from raw FASTQ reads through initial inspection, preprocessing and primary sequence analysis.
FASTQPrimary analysisNGS
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AL
Reads Alignment with Bowtie, Bowtie2, BWA, HISAT2 and STAR
Example alignment workflows covering widely used short-read and RNA-seq aligners for different data types.
BowtieBWASTAR
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DD
Removing Duplicated Sequences from FASTA Files
Identify and remove duplicate FASTA entries while keeping sequence collections clean and non-redundant.
FASTADeduplicationShell
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TR
Trimming and Filtering of NGS Reads
Trim adapters and filter low-quality sequencing reads before alignment or other downstream analyses.
TrimmingFilteringFASTQ
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Practical reference library. Commands may need adjustment for software versions, genome builds, file naming conventions and the requirements of a specific dataset.