ATpoint

library(biomaRt)

## get mouse transcript coordinates
mmusculus_genes <- getBM(attributes = c("ensembl_gene_id", "chromosome_name",
                                        "transcript_start", "transcript_end"),  
                         mart = useMart("ensembl", dataset = "mmusculus_gene_ensembl"))

## put in the exact same format as the example of the toplevel question,
## not caring about the fact that hgnc is not the correct name for mouse genes:
large.input <- data.frame(chrom = mmusculus_genes$chromosome_name,

ATpoint

##
library(rtracklayer)

## Use rtracklayer to import a subset of a bigwig file from disk into R.
## reference.gr is a GRanges object with the ranges that will be used for subsetting
## selected.gr is a GRanges object with the count data for each interval stored in elementMetadata(selected.gr)
selected.gr <- rtracklayer::import(Path.To.BigWig, format = "BigWig", selection = BigWigSelection(reference.gr))

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require(data.table)
require(microbenchmark)
require(GenomicRanges)

x <- fread("
    chrom   start   end hgnc
    1   100 200 MYC
    1   150 300 MYC
    1   400 500 MYC
    1   150 230 TP53

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library(biomaRt)

## How to get gene coordinates starting from Entrez gene IDs:

## Example for human:
GeneName <- "hgnc_symbol"            ## for mouse use "mgi_symbol"
DataSet  <- "hsapiens_gene_ensembl"  ## for mouse use "mmusculus_gene_ensembl

## Create a look-up table using biomaRt:
Coords <- mmusculus_genes <- getBM(attributes = c("entrezgene_id", 

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## Script to create a transcriptome fasta file that contains both spliced and unspliced
## transcripts based on a GTF file from GENCODE.
## Also see the preprint https://doi.org/10.1101/2020.03.13.990069 from Charlotte Soneson on the matter of
## how preprocessing influences the outcome of velocity analysis.
## The below steps are inspired by the preprint and personal correspondence with CS.

ANALYSISDIR="./"

dir.create(paste0(ANALYSISDIR, "/Alevin_IDX"))

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library(GenomicRanges)
library(matrixStats)

ranges1 <- GRanges(seqnames = c("chr1", "chr2", "chr3"),
                   ranges = IRanges(start=c(1,100,1000),
                                    end = c(10,150,5000)))

ranges2 <- GRanges(seqnames = c("chr1", "chr2", "chr3"),
                   ranges = IRanges(start=c(11,110,2000),
                                    end = c(20,130,3000)))

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#/ A minimal example on how to use EnrichedHeatmap together with rtracklayer.
#/ Required data are at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111902
#/ Go for the files :
#/ "GSM3045250_N_ATAC_Kaech_1_peaks.broadPeak.gz" and (genomic regions in BED-like format)
#/ "GSM3045250_N_ATAC_Kaech_1.bw"                     (the bigwig files with read counts)

require(EnrichedHeatmap)
require(rtracklayer)
require(circlize)
require(data.table)

ATpoint

metaBigBam.c:485:12: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
    if (h->cigar_tab == 0) 
           ^
/usr/local/include/htslib/sam.h:75:29: note: 'cigar_tab' has been explicitly marked deprecated here
    const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
                            ^
/usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
                                                ^
metaBigBam.c:487:5: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]

ATpoint

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:

ATpoint

FATAL:   container creation failed: unable to copy files to container fs: while copying [environment.yml] to /tmp/rootfs-4b4c7b49-9f72-11eb-a808-12cf446d2005/environment.yml: exit status 1: /bin/cp: cannot stat 'environment.yml': No such file or directory
FATAL:   While performing build: while running engine: while running /usr/local/libexec/singularity/bin/starter: exit status 255
FATAL:   While performing build: build image size <= 0