reads_list: Reads information data table

In LabTranslationalArchitectomics/riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

Reads information data table

Description

An example dataset containing details on reads mapping on the mouse transcriptome, generated from BAM or BED files. A subset of the original dataset is provided, including only reads aligning on the translation initiation site. Please contact the authors for further information.

Usage

reads_list

Format

A list of data tables with 1 object (named Samp1) of 100,062 rows and 6 variables:

transcript

Name of the transcript (ENST ID and version, dot separated)

end5

Position of the 5' end of the read with respect to the first nucleotide of the transcript, in nucleotides

end3

Position of the 3' end of the read with respect to the first nucleotide of the transcript, in nucleotides

length

Length of the read, in nucleotides (intended as the width of the reference sequence region covered by the RNA fragment. For further information about this choice please refer to section Details of function bamtolist)

cds_start

Leftmost position of the annotated CDS with respect to the first nucleotide of the transcript, in nucleotides

cds_stop

Rightmost position of the annotated CDS with respect to the first nucleotide of the transcript, in nucleotides

LabTranslationalArchitectomics/riboWaltz documentation built on Jan. 17, 2024, 12:18 p.m.