TUTORIAL: Transcriptome Assembly

Preprocessing of RNA sequencing reads

October 31, 2021

Transcriptome sequencing read files

DATASET: Fakankun I et al. (2019) Ph.D. thesis, University of Manitoba (in progress) Rhodosporidium diobovatum.
This dataset is a random sample of about 5% of the reads from fungal RNAseq. Cells were grown in conditions of nitrogen starvation for 18 or 24 hours. Three replicate cultures were done for each time point.

Remember: save these files to your reads directory.

raw read files (Illumina, paired end)	time	replicate
HI.3992.004.Index_1.18-1_R1_S5.fastq.gz HI.3992.004.Index_1.18-1_R2_S5.fastq.gz	18 h	1
HI.3992.004.Index_3.18-2_R1_S5.fastq.gz HI.3992.004.Index_3.18-2_R2_S5.fastq.gz	18 h	2
HI.3992.004.D701---D503.18-3_R1_S5.fastq.gz HI.3992.004.D701---D503.18-3_R2_S5.fastq.gz	18 h	3
HI.3992.004.Index_8.24-1_R1_S5.fastq.gz HI.3992.004.Index_8.24-1_R2_S5.fastq.gz	24 h	1
HI.3992.004.Index_10.24-2_R1_S5.fastq.gz HI.3992.004.Index_10.24-2_R2_S5.fastq.gz	24 h	2
HI.3992.004.Index_11.24-3_R1_S5.fastq.gz HI.3992.004.Index_11.24-3_R2_S5.fastq.gz	24 h	3