Perl: Preparation of FASTA and GTF files for RNA-seq

Abstract: The FASTA and GTF/GFF format files should be prepared when genome mapping using the aligner.

NGS: Why is the logarithm of expression level determined by RNA-seq?

Abstract: Expression levels determined by RNA-seq are count-based. For expression level analysis, logarithm of read counts is more usual than read counts directly.

NGS: Notes of Piwi-interacting RNA (piRNA)

Abstract: Statistics of piRNA

NGS: Notes of microRNAs

Abstract: Names and statistics of miRNAs the in miRNA data base.

NGS: Count reads for mRNA-seq

Abstract: Counting how many read mapped to the genome features (gene, transcript, or exon) is a common task for mRNA-seq analysis.

NGS: Saturation analysis for RNA-seq

Abstract: How is the expression profiling from RNA-seq deep enough? Or How many multiplexing samples can be in one lane?

NGS: Base Quality of Sequencing

Abstract: The base quality provide important information of sequencing quality.

NGS: Interpretations of SAM format

Abstract: Howe to analyze SAM files.

NGS: Coverage of sequencing

Abstract: Coverage of sequencing is one important issue of evaluating sequencing depth in the design of high-throughput sequencing experiments.

Parallel computing using multi-threads

Abstract: Multi-threading programming can speed up analytic work.

NGS: Get sequences from raw data

Abstract: Sequencing raw data in FASTQ format is a crucial starting point of NGS data analysis. Here, I show how to extract read sequences from FASTQ files.