Open sroener opened 1 year ago
IanCodes
commented
1 year ago I discovered this problem recently. I appears that the runIchorCNA.R file for v0.5.0 only contains the run_ichorCNA() function. This means it cannot be run using Rscript. I have tried using the script from v0.3.2.
ycl6
commented
1 year ago Hi @sroener
With ichorCNA v0.5, the analysis need to be performed inside R using the run_ichorCNA function. Below is an example that I adapted from that you provided.
Also, you'll need to get a copy of the repTime wig from inst/extdata, e.g. Koren_repTiming_hg38_1000kb.wig that I used in the example.
ichorCNA::run_ichorCNA(id = "test19_processed",
tumor_wig = "results/testrun/icorCNA/readcounts/test19_index_processed.hg19.wig",
gcWig = "resources/ichorCNA/gc_hg19_1000kb.wig",
mapWig = "resources/ichorCNA/map_hg19_1000kb.wig",
repTimeWig = "Koren_repTiming_hg38_1000kb.wig", # Get it from "inst/extdata"
normal_panel = "resources/ichorCNA/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds",
centromere = "resources/ichorCNA/GRCh37.p13_centromere_UCSC-gapTable.txt",
ploidy = "c(2,3)",
normal = "c(0.5,0.6,0.7,0.8,0.9)",
maxCN = 5,
scStates = "c(1,3)",
chrs = 'c(1:22,"X")', # default
chrTrain = "c(1:22)", # default
estimateNormal = TRUE, # default
estimatePloidy = TRUE, # default
estimateScPrevalence = TRUE, # default
includeHOMD = FALSE, # default
txnE = 0.9999,
txnStrength = 10000,
plotFileType = "png",
genomeBuild = "hg19",
genomeStyle = "UCSC",
outDir = "results/testrun/icorCNA/test19_processed_hg19", # Folder need to exist
)
sroener
commented
1 year ago Hi @ycl6
thank you for your answer.
Could you provide a little background on what Koren_repTiming_hg38_1000kb.wig does?
In the past I used ichorCNA in a pipeline using the runIchorCNA.r CLI in a rule for processing a huge amount of samples. As I think that providing CLIs and functional interfaces for end-to-end tools, I am wondering whether there is a particular reason for dropping the CLI?
ycl6
commented
12 months ago Hi @sroener
repTiming takes a wig file that has replication timing data. Amnon Koren is a leading researcher of this field and you can see a figure on his website that illustrate how replication timing influences copy number along a chromosome during DNA replication. Like other CNA tools, correction for replication timing can be enabled to better profile CNV events. Ideally, you will/can use the replication timing data from your cell/tissue type (assayed using Repli-seq or inferred from WGS) to perform correction. Though, replication timing is highly conserved, you can try publicly available resources, such as that provided here. @gavinha can probably share where the replication timing tracks were sourced and how they were converted into wig files.
The repTimeWig param should be an optional input but a bug with the current version means you do need to supply one. You can try PR https://github.com/GavinHaLab/ichorCNA/pull/15 and that should allow you to run ichorCNA without replication timing wig.
@gavinha can probably explain why the CLI version is dropped (or not have a script to work alongside the current run_ichorCNA function). It is not too difficult to write one to work with the current version. I can chip in if the maintainer does not already have one.
lbeltrame
commented
9 months ago It would be very useful to have a working CLI. Otherwise, to work in containers during workflows (e.g. in nextflow, snakemake, WDL, you name it), everyone would need to reinvent the wheel.
xiucz
commented
7 months ago Hi, @ycl6 Do you know how to create a repTimeWig file? I need a 50kb binsize file for hg19, but I have found very limited information online.
Best, xiucz
ycl6
commented
7 months ago Hi @xiucz
You might want to contact @gavinha and ask how he creates the repTimeWig files provided in this repo.
One of the repTimeWig files is in 50kb binsize: Koren_repTiming_hg19_50kb.wig
https://github.com/GavinHaLab/ichorCNA/tree/master/inst/extdata
Hi,
I have been updating my ichorCNA version and now I get the following error:
This happens both with the full command or just with
runIchorCNA.r --help.Full command:
ichorCNA was installed via bioconda:
The final environment looks like this:
Help would be appreciated!