Alva Rani James

Reads covered by variants

1

Hello All, This is not an issue, but I have a technical question. I wanna find the reads covered by each variant in the simulated truth VCF file. And I...

Hello All, Cufflinks is not recognizing the option --library-norm-method while finding the transcript abundance. while using it on the following command line cufflinks --num-threads 10 --quiet --no-update-check --max-bundle-frags 2000000 --library-type...

preprocess_features.py file is generating empty output bed files

2

Hi All, Thanks for the tool. I am a beginner in deep learning. I was trying to reproduce the tutorials with the provided datasets. I have started with this https://github.com/davek44/Basset/blob/master/tutorials/prepare_compendium.ipynb...

Not able to install on Mac book M1

5

I am trying to install fastp tool on my Mac M1. So far, I have tried all these options download `osx-64_fastp-0.23.4-h5712c04_2.tar.bz2` then, `conda install osx-64_fastp-0.23.4-h5712c04_2.tar.bz2` The fastp file is not...

Not able to reproduce the best fit PRS for plink

17

Hi Sam, Thanks for the great tutorial. I have been trying PLINK for the polygenic risk score. However, with the height dataset and EUR plink files, I am not able...

Vcfv4.2 vcf reader parser complaints while parsing through vcf file

2

I have 40 vcf files, which I need to convert into a tabular format. But the vcf.reader parser complaints while I am parsing it through each row. The same script...

Dear All, I have followed the steps to set up a virtual env in R for spacy. https://www.rdocumentation.org/packages/spacyr/versions/1.3.0 However, at this step, Install spaCy language models, I am getting the...