Before running GROseq pipeline you will need to obtain genome(fasta), bowtie index (.bt2), chromosome sizes (.chrom.sizes) and annotation.
GRO-seq allows us to profile the distribution of nascent RNAs across the genome and analyse the activity of RNA polII.
install cutadapt using the instruction from this page.
cutadapt -a AACCGGTT -o output.fastq input.fastq
install STAR from thing github repository.
[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