Ferrari RR, Batista TM, Zhou QS, Hilário HO, Orr MC, Luo A, Zhu CD. The Whole Genome of Colletes collaris (Hymenoptera: Colletidae): An Important Step in Comparative Genomics of Cellophane Bees. Genome Biol Evol. 2023 May 5;15(5):evad062. doi: 10.1093/gbe/evad062. PMID: 37075227; PMCID: PMC10159585.
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
This protocol provides detailed, step-by-step instructions for students and researchers to assemble transcriptomes from short reads generated by Illumina technology. In this tutorial, we will check the quality of the sequencing data and align the reads with a bacterial genome database to eliminate potential contamination. We will then use two approaches to assemble the transcripts: de novo assembly and alignment to the reference genome. The transcripts will be quantified and the assemblies evaluated.
/data/kiko/thiagomafra/reads/R2015100B_L3_139A39.R2.fastq.gz 2>&1 | tee redundans.log
TRANSCRIPT QUANTIFICATION
TRANSCRIPT QUANTIFICATION
****Trinity (using Kallisto)****
***Estimating transcript abundance (on headnode)***
#Use trimmed reads (.fastq.P.qtrim) if --trimmomatic was used in the assembly (the 'index' and 'quantification' functions of Kallisto are performed here)
**Estimate transcript abundance (using a built-in Kallisto)**
*Prepare the reference + run the estimation using (on headnode)*
#Use trimmed reads (.fastq.P.qtrim) if --trimmomatic was used in the assembly (the 'index' and 'quantification' functions of Kallisto are performed here)