smith: Ribosome profiling and RNA-Seq library from Smith et. al.

In celalp/ribofootprintR: Fast data extraction and visualization from .bam files for ribosome footprint profiling experiments

Description

Ribosome profiling and RNA-Seq libraries from WT S.Cerevisiae.

Usage

data("smith")

Format

This is the results of the read_profiling_data function. In addition to the n and rna elements the genedf and DNAStringset is present in smith$genedf and smith$seq

Details

These libraries are prepared in the presence of cycloheximide. The data is published by Smith et. al. PMID: 24931603. The raw data can be accessed at SRR125839 for ribosome profiling and SRR12558470. The alignment was done to an earlier version of yeast transcriptome that was generated manually. A similar transcriptome and genedf can be generated using generate_transcriptome function.

Alignment was done with:

lib=$(find -iname "*.fastq")

for i in ${lib[*]}

do

cutadapt -a CTGTAGGCA -q 10 --trim-n -m 10 -o $i-trimmed.fastq $i

bowtie -m 100 -p 8 -n 2 -l 15 --un $i-norna transcriptome/rna $i-trimmed.fastq

bowtie -m 4 -p 8 -n 2 -l 15 -S --best --strata transcriptome/profiling $i-norna > $i.sam

samtools view -b $i.sam > $i.bam

samtools sort $i.bam > $i-sorted.bam

samtools index -b $i-sorted.bam > $i-sorted.bam.bai

done

Source

https://www.ncbi.nlm.nih.gov/pubmed/24931603

References

Cell Rep. 2014 Jun 26;7(6):1858-66

Examples

data(smith)

celalp/ribofootprintR documentation built on May 12, 2019, 12:04 p.m.