Alignment of a Ribo-seq dataset against Leishmania donovani (HU3) genome

Description

The origin of the samples and the ribosome-footprint methodology are described in the article by Bifeld et al., 2018 (PMID: 30505948). Raw sequencing reads (Illumina single-end reads in FASTQ format) were downloaded at the NCBI Sequence Read Archive (SRA), under project number PRJNA495919. In particular, the 24,741,340 (1×76 nucleotides) Ribo-Seq reads from sample ID sample SRR8040414 (derived from L. donovani promastigotes, control sample) were used to prepare this dataset. Trimmomatic tool (Bolger et al., 2014; PMID: 24695404) was used to clip adapters. Additionally, rRNA-containing reads were filtered after aligning them against the rRNA sequences existing in the L. donovani genome by using the BWA-MEM aligner (Li, 2013; ArXiv ID: 1303.3997v2) according the sqtk3 pipeline (https://github.com/lh3/seqtk). The L. donovani genome used as reference (Camacho et al., 2019; PMID: 30992521) is available thought the following Mendeley dataset: https://data.mendeley.com/datasets/b82fm2w2h9/2. Thereafter, the BWA-MEM aligner was used to map remaining reads to the genome and the resulting alignment files were sorted and indexed using SAMtools (Li et al., 2009; PMID: 19505943). This final file (and its accompanying bam.bai) is linked to this dataset.

Steps to reproduce

Use a genome viewer (IGV or similar)

Institutions

Categories

Funding

Licence