loukesio / GRO-seq

Before running GROseq pipeline you will need to obtain genome(fasta), bowtie index (.bt2), chromosome sizes (.chrom.sizes) and annotation.

GRO-seq

GRO-seq allows us to profile the distribution of nascent RNAs across the genome and analyse the activity of RNA polII.

1. Remove/Trim a 3’ adapter, Cutadapt

install cutadapt using the instruction from this page.

cutadapt -a AACCGGTT -o output.fastq input.fastq

2. Remove rRNAs using STAR

install STAR from thing github repository.

3. Using Tallymer and Genome tools

http://genometools.org/

References

[1] https://github.com/vari-bbc/GROseq_scripts/blob/main/GROP_20190515_GroSeq.Rmd
[2] https://github.com/vari-bbc/GROseq_scripts/blob/main/GROP_20190515_GroSeq.sh
[3] https://nf-co.re/nascent
[4] https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02349-4
[5] https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md
[6] https://scientiasalut.gencat.cat/bitstream/handle/11351/6516/proapoptotic_gene_interferon_regulatory_factor_1_mediates_antiproliferative_outcome_paired_box_2_gene_tamoxifen_2020_material_suplementari.pdf?sequence=2&isAllowed=y