te_riboseq_atlas's Introduction

TE RiboSeq Atlas (Dopkins)

A transposable element atlas of ribo-seq data from multiple tissue types. (Project ID: PRJNA756018)

To get DAG:

snakemake --profile profiles/aws  --forceall --dag | dot -Tpdf > dag.pdf

To get rule graph:

snakemake --profile profiles/aws  --forceall --rulegraph | dot -Tpdf > rulegraph.pdf

To get file graph:

snakemake --profile profiles/aws  --forceall --filegraph | dot -Tpdf > filegraph.pdf

To run pipeline:

snakemake --profile profiles/aws/ all

To run only Telescope in a sample-specific manner:

snakemake --profile profiles/aws/ results/telescope/{sampleid1}_telescope_completed.txt results/telescope/{sampleid2}_telescope_completed.txt

To run only hervquant in a sample-specific manner:

snakemake --profile profiles/aws/ results/salmon/{sampleid1}_salmon_completed.txt results/salmon/{sampleid2}_salmon_completed.txt

Example to run both hervquant and telescope for 3 samples:

snakemake --profile profiles/aws results/telescope/SAMN20849944_telescope_completed.txt results/salmon/SAMN20849944_salmon_completed.txt results/telescope/SAMN20849945_telescope_completed.txt results/salmon/SAMN20849945_salmon_completed.txt results/telescope/SAMN20849946_telescope_completed.txt results/salmon/SAMN20849946_salmon_completed.txt

Reference genomes used for telescope and hervquant:

For a full list of reference genomes used, please refer to the config.yaml file. For STAR, we used GRCh38.d1.vd1.fa.tar.gz. For Telescope, we used retro.hg38.v1.gtf. For hervquant, we used the reference from the original paper, which can be found here and here.

To modify pipeline:

Change sample download table, or change the reference genomes in the config.

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