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Hi Jpuntomarcos:
Thank you for developing the CNVfilter algorithm.
I want to know whetherCNVfilteR algorithm can be applied to WES data of tumor samples. We know that for tumor samples, we ne…
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Dear Professors@wtwt5237:
Recently,I have been learning this pipeline,and hope to transplant it in our own data.However,I have some questions about the input data in the somatic.pl.Why you set …
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Can I combine the read count that both from TCGA and GTEx, and then perform DEG analysis directly without remove batch effect in your provided count data? Or I can only perform DEG analysis via DESeq2…
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Survival analysis (Cox regression and ggforest plot)
- 25 different tumors and no cancers
- PTV burden as a continuous variable
- Variables in the Cox models: sex, ethnic group, PCA1-10, PTV burd…
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I notices the notes in the README file said "2. If you don't have normal samples to build baseline(baseline step for tumor only sample detection), you can download the microsatellites information with…
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I thought this would be interesting to have, as described in:
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php
…
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There is a mismatch on how some properties are named.
For example `tumour: true` is sometimes called `is_tumour: true`
elevu updated
3 weeks ago
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if `-index 1` is passed with `-p flag`, only one split file is flagged:
```
$ caveman.pl --version
VERSION: 1.16.0
$ ls -lah /tmpCaveman/
Aug 11 20:12 .
Aug 11 20:12 ..
Aug 11 20:11 alg_bea…
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### Description of feature
CNVKit can take sex information: https://github.com/etal/cnvkit/blob/b218280edb266788ea8326596d4283183ce425ea/doc/sex.rst as well as SNP information to to infer b-allel f…
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### Description of the bug
As seen in the attached log file, the pipeline stops working and cycles in error with amazonaws. I am new to nf-core so I am unfamiliar with how all the parts of the pipeli…