BED format is a simple way to define basic sequence features to a sequence. It consists of one line per feature, each containing 3-12 columns of data, plus optional track definition lines. These are generally used for user defined sequence features as …

The latest stable build of RNA-SeQC is available on the GitHub Releases page, and contains static binaries for Linux and OSX. RNA-SeQC is also available as a docker image: gcr.io/broad-cga-aarong-gtex/rnaseqc:latest which is automatically updated with any code change.

bedtools getfasta extracts sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file. 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file. 2. You can use the UNIX fold command to …

RNA-seq coverage analysis. Thanks to Erik Minikel. Identifying targeted regions that lack coverage. Thanks to Brent Pedersen. Calculating GC content for CCDS exons. Making a master table of ChromHMM tracks for multiple cell types.

I making a bed file for RSeQC, so it can do things like compute the number of reads from exons, introns, 5"UTRs, etc. I want to use a bed file that corresponds to my GTF file, so I use gtf2bed to ...

Oct 30, 2019 · In this guide, we explore the most common file formats used in the field, including BED and BAM, and provide tips for optimizing your analysis efforts.

Certain workflows allow or require you to import a targeted regions file, also known as a BED file, within the Reference Sequence screen. BED files are used to define capture regions in the assembly, and can be generated by the sequence provider or made by hand.

Oct 16, 2022 · RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.

Jul 4, 2014 · Application of sequencing to RNA analysis (RNA-Seq, whole transcriptome, SAGE, expression analysis, novel organism mining, splice variants)

Mar 22, 2015 · I have two file: one is genome.fa and the other is RNA-seq.fa. Following is the RNA-seq.fa format. Anyone can recommend the appropriate software to produce the *.bed file?