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ASCAT could not find an optimal ploidy and purity value for sample logR. #174
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I am waiting for your answer. Would you please add your comments for this issue. |
Hi, did you do GC correction before the PCF segmentation? Please check the exact steps in the example folder under this link https://github.com/VanLoo-lab/ascat/tree/master/ExampleData. |
Thanks for the immediate reply. ASCAT run without matched normal data (platform needs to be adapted, see ?ascat.predictGermlineGenotypes)
if not please let me know. I guess the follwoing line should be the correction step which actaully i missed here you are using "GC_example.txt" and "RT_example.txt" |
Yes. If you do not normal sample, that's the steps you should follow. You could try the GC and RT example data from the GitHub to check if it works. Please be careful about the hg19/hg38 version of your data. |
afetr running the follwoing code
got this error: I tried using "hg19" genomeversion and got the same error. |
would you please reply |
Hi, could you attach a piece of your data? I need more details to figure out the issue. |
here I am ataching a zip folder that contains the follwoing files
Here is follwoing code I am running Create ASCAT object using the nucleotide counts
The output logR and BAF files from the above step are processed with ASCAT without matched normal data protocol
GC correction
here is the error Please let me know if you need any other information. Happy to provide |
Hello Zhang, |
Hi, the format of your rowname in both logR and BAF is wrong. You need to format the rownames of BAF and logR as for example "1_23456", the chromosome and position are seperated by "_". I reformat your data and tested on my end. They worked. |
Hello I am I am facing this error while running this function.
ascat.runAscat(ascat.bc)
Warning message:
In runASCAT(lrr, baf, lrrsegm, bafsegm, ASCATobj$gender[arraynr], :
ASCAT could not find an optimal ploidy and purity value for sample logR.
Here I am exaplning the detailed process I have carried out.
# Genertating the nucleotide counts from maftools
maftools::gtMarkers (t_bam = Sample_12614-11016.bam", build = "hg38", prefix="chr", fa= "ucsc_hg38")
# Create ASCAT object using the nucleotide counts.
ascat.bc = maftools::prepAscat_t(t_counts = "Sample_12614-11016_nucleotide_counts.tsv", min_depth = 15, sample_name = "tumor_only")
This is tumor sample and hence used "tumor_only". This process genrated the following files
tumor_only.tumour.logR.txt
tumor_only.tumour.BAF.txt
The output logR and BAF files were processed with ASCAT without matched normal data protocol
ASPCF segmentation
Warning message:
In runASCAT(lrr, baf, lrrsegm, bafsegm, ASCATobj$gender[arraynr], :
ASCAT could not find an optimal ploidy and purity value for sample logR.
I did not get this error with some other samples and I am able to run successfully with further steps.
you may follow the link to view the files
[https://drive.google.com/drive/folders/1iN02Z6i9hkh8g3kdkH_ZY7P1qovGmYcT?usp=sharing]
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