Genome information was download from Ensembl. Samtools [1]
and Picard [2] were used to index genome sequences.
Agat [3] was used to correct common issues found in Ensembl
genome annotation files. Salmon [5] was used to preduce and index a
decoy-aware gentrome based on both DNA and cDNA sequences.
Raw fastq files were trimmed using Fastp [4]. Salmon [#salmonpaper]
performed the pseudo-mapping and estimation of transcripts abundance. The count
aggregation was performed with tximport [#tximportpaper].
The whole pipeline was powered by Snakemake [7].
This pipeline is freely available on Github, details about installation
usage, and resutls can be found on the Snakemake workflow page.
| [1] | Li, Heng, et al. "The sequence alignment/map format and SAMtools." bioinformatics 25.16 (2009): 2078-2079. |
| [2] | McKenna, Aaron, et al. "The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data." Genome research 20.9 (2010): 1297-1303. |
| [3] | Dainat J. AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format. (Version v0.7.0). Zenodo. https://www.doi.org/10.5281/zenodo.3552717 |
| [4] | Chen, Shifu, et al. "fastp: an ultra-fast all-in-one FASTQ preprocessor." Bioinformatics 34.17 (2018): i884-i890. |
| [5] | Patro, Rob, et al. "Salmon provides fast and bias-aware quantification of transcript expression." Nature methods 14.4 (2017): 417-419. |
| [6] | Love, Michael I., Charlotte Soneson, and Mark D. Robinson. "Importing transcript abundance datasets with tximport." Dim Txi. Inf. Rep. Sample 1.1 (2017): 5. |
| [7] | Köster, Johannes, and Sven Rahmann. "Snakemake—a scalable bioinformatics workflow engine." Bioinformatics 28.19 (2012): 2520-2522. |