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Hi there, I wonder if the PEPPER-Margin-DeepVariant pipeline can work well on RNA variant calling or not?
DeepVariant doesn't have an RNA seq model but users may try the exome model... https://githu…
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Hi Christoffer,
I have a sample which has very low purity (WS9-T in the figure below). When I run superFreq it predicts that it has very high ploidy, which I know isn't likely because a sample from…
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Hi,
I am trying to plot the clones using TimeScapes (http://bioconductor.org/packages/release/bioc/html/timescape.html) but not sure how to calculate the clonal prevalence. I was tying to take ave…
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Hi Again Christoff-
So I just tried to run on a multiregion case that I have - 14 WGS samples total and when it got to the clonality part of the pipeline I threw the following error:
`Error in i…
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I'm trying to have superFreq output to an absolute path rather than using the base path where the bam files for the quality contorl samples are. The line below seems to force creation of the R and plo…
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Hi,
Thank you for providing this amazing tool! I am a newbie using it, but I could start with the basics. I've got clones in my data with different CNV profiles. Analyzing the single-cell RNA-seq dat…
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Dear Nick,
Sorry if this is naive question. Which function in the package can closely calculate clonal expansion per sample as in the bulk TCR data, please?
Thank you
Sa753 updated
3 years ago
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https://mp.weixin.qq.com/s/I50fYtrGl_bp_Qoy_R1K-Q
ixxmu updated
2 years ago
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@mourisl, thank you so much again for this wonderful tool and for answering questions so promptly. I had a question about how to interpret the CPK metric from trust-stats.py. Essentially, I am wonde…
kc199 updated
3 years ago
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Hi
thanks for the modification compressed fastq it seem to work perfectly but i have another problem.
The identification step seem to don't work at all.
immunedb_identify /share/configs/my_db.js…