scRNAsim

The projects implements a simulation of single cell RNA sequencing (scRNA-seq), accounting for some common sources noise that complicate the analysis of the resulting data.

Setting up the virtual environment

Create and activate the environment with necessary dependencies with Conda:

conda env create -f environment.yml
conda activate scrnasim

Workflow

The workflow makes use of the tools available in the scRNAsim-toolz repo. These are:

1. Transcript sampler
2. Structure generator
3. Sequence extractor
4. Priming site predictor
5. cDNA generator
6. Fragment selector
7. Read sequencer

Inputs:

1. Genome annotation file (gtf) (#1)
2. Average gene expression values (csv: geneID,count) (#1)
3. Total number of transcripts to samples (#1)
4. Probability of intron inclusion (#2)
5. Genome sequence file (fasta) (#3)
6. Length of poly(A) tails (#3)
7. Primer sequence (#4)
8. Threshold for the energy of primer-mRNA interaction needed for priming (#4)
9. Mean of fragment length (#6)
10. SD of fragment length (#6)
11. Read length (number of sequencing cycles) (#7)

Outputs:

1. Representative transcripts (gtf) (#1)
2. Representative transcript counts (csv: transcriptID,count) (#1)
3. Sampled transcripts (gtf) (#2)
4. Sampled transcript counts (csv: transcriptID,count) (#2)
5. Transcript sequences (fasta) (#3)
6. Annotated internal priming sites (gtf) (#4)
7. Unique cDNA sequences (fasta) (#5)
8. cDNA count table (csv) (#5)
9. Terminal fragment sequences (fasta) (#6)
10. Read sequences (fasta) (#7)