FAstqc DAta PArser - A minimal parser to parse FastQC output data.
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Updated
Apr 9, 2016 - Jupyter Notebook
FAstqc DAta PArser - A minimal parser to parse FastQC output data.
An R package to parse and manage text output of the sequencing quality control utility (fastQC)
Report the mean quality score per base from the output of FastQC.
Classification of RNA-Seq samples using circRNA expression
Script to clean Illumina pair-end sequences produced with the Nextera kit. Bases below Q30, Ns, and Nextera adapters are removed. Bases can also be removed at the beginning and end of each sequence. At the end, clean files can be analyzed with FastQC.
Complete Pipeline for RNA-seq data analysis: From FastQ to differntial gene expression to annotated Variations.
Estimate fastq-formatted read abundace in RNA-Seq analysis with Kallisto
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
Count your fastq-formatted rna-seq reads with Salmon
Qiime2 and DADA2 are one of the latest bioinformatics tools used in 16S RNA analysis. The current Qiime2 and DADA2 pipelines support End to End 16S RNA analysis, among other analyses.
Map and post-process your bams for SNP calling
Snakemake workflow for Salmon quantification and FastQC quality controls
Exploring Bioinformatics pipelines
Python code to compute adatper content in reads, kmer content, per-base-GC content (at a specific position in a read alignment, against reference genome), per base NC content (at a specific position in a read alignment against the reference genome), per base seq quality (across aligned reads), per base sequence content, per base quality scores, …
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