Repository of the code to reproduce analysis and figures for "Intergenic RNA mainly derives from nascent transcripts of known genes". bioRxiv, 2020.
- stringtie
- igvtools
- gffcompare
- R
R packages requirements:
- GenomicFeatures
- rtracklayer
- data.table
- ggplot2
- ggpubr
- cowplot
- ggthemes
- ggsci
- ggforce
- ggExtra
- ggrepel
- scales
- DT
- circlize
- BSgenome.Hsapiens.UCSC.hg38
- ggbio
- phastCons100way.UCSC.hg38
- GenomicAlignments
- genomation
- VennDiagram
- viridis
Pre-processing, alignment to the human reference genome and generation of the individual transcriptome assemblies for each dataset have been performed with the RNA-seq-pipeline; the Supplementary Table 1 contains all the accession codes of the datasets used for annotation and validation.
The output files obtained with this procedure should be placed in the following folders:
- stringtie: GTF files produced by stringtie;
- counts: QoRTs folders (containing the QC.geneCounts.detailed.txt.gz and QC.summary.txt files) and StrandCheck.out.tab files;
- RNAseq_bw: stranded (plus and minus) CPM normalised bigWig files;
- RNAseq_bam: BAM files (post-deduplication).
Parsing of the Gencode v27 reference annotaion and generation of the R objects used in this analysis have been performed with the R_Gencode_Reference processing scripts.
The R objects obtained with this procedure should be placed in the GencodeReference folder (default); otherwise, change the annotationFolder path using their location on the current machine.
The main code is in R markdown format (Rmd), which can be opened and executed via R studio or other compatible editors, and it is subdivided into multiple 'chunks', thus providing the ability to execute the different tasks step-by-step.
- Gencode v27 + Intergenic TUs (all)
- Download Genomic Track (Bed or BigBed)
- View in UCSC Genome Browser
- Gencode v27 + Intergenic TUs (HeLa)
- Download Genomic Track (Bed or BigBed)
- View in UCSC Genome Browser
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- Download Genomic Track (Bed or BigBed)
- View in UCSC Genome Browser
-
- Download Genomic Track (Bed or BigBed)
- View in UCSC Genome Browser
-
- Download Genomic Track (Bed or BigBed)
- View in UCSC Genome Browser