Error processing CAGE data using CagefightR
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18 months ago

Hi everyone,

I am trying to process some CAGE data from Drosophila using CAGEfightR but I am having the following error. Has anybody seen this before? I cannot find anything related on internet.

This is the code I am using:

```

library(CAGEfightR)

bsg <- BSgenome.Dmelanogaster.UCSC.dm6

txdb <- TxDb.Dmelanogaster.UCSC.dm6.ensGene

odb <- org.Dm.eg.db::org.Dm.eg

bw_plus <- "/n/projects/sga/analysis/CAGE_data/cage_pos.bw"

bw_minus <- "/n/projects/sga/analysis/CAGE_data/cage_neg.bw"

bw_plus <- BigWigFileList(bw_plus)
bw_minus <- BigWigFileList(bw_minus)
names(bw_plus) <- names(bw_minus) <- "kc167_CAGE-seq_rep1"

genomeInfo <- SeqinfoForUCSCGenome("dm6")

CTSSs <- quantifyCTSSs(plusStrand=bw_plus, minusStrand=bw_minus, genome=genomeInfo)

Checking supplied genome compatibility...

Iterating over 2 genomic tiles in 1 samples using 38 worker(s)...

Importing CTSSs from plus strand...

Importing CTSSs from minus strand...

Merging strands... Error in .check_GenomicRanges_for_coercion_to_GPos(from, "UnstitchedGPos") :
all the ranges in the object to coerce to UnstitchedGPos must have a width of 1

Thanks!

CAGE-seq CAGEfightR software error • 309 views
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