myvariant Posts

A: Can I compare TPM values for a transcript across different transcriptome assembl by JC ♦ 8.0k
> I cannot find any literature or posts in regard to this, if you can point me to any resource...
C: Empty VCF files produced by both Mutect2 and HaplotypeCaller? by igor ♦ 8.0k
This might the same problem/solution: https://www.biostars.org/p/390639/
C: Calculate disease risk based on the genoytype of some SNPs? by miguelcarnero • 0
First of all I would like to thank you very much for both the answer and help. Unfortunately, thi...
C: Ideas on how to evaluate genomic coordinates remapping tools? by igor ♦ 8.0k
I think what Wouter meant is that you have to call variants using the other version of the refere...
C: Mutect2 (GATK4, Java8) outputs empty VCF file for tumor only mode by igor ♦ 8.0k
You can also use GATK to adjust the MAPQ scores. From [Calling variants in RNAseq][1]: > STAR...
C: Ideas on how to evaluate genomic coordinates remapping tools? by igor ♦ 8.0k
Interesting. How would it work without chain files?
C: Ideas on how to evaluate genomic coordinates remapping tools? by juliette • 20
I understand that, however I'm in the process of developing a remapping tool that doesn't use cha...
C: Ideas on how to evaluate genomic coordinates remapping tools? by igor ♦ 8.0k
I am not sure how much of a difference the tools introduce, especially for single-nucleotide posi...
C: How to remove outliers using PCA in R? by zhaoliang0302 • 0
Thanks, I save this plot as PDF file (large size) and then zoom in to get the outlier samples. It...
C: Fast download of FASTQ files from the European Nucleotide Archive (ENA) by RamRS ♦ 22k
Please do not add Answers, they do not serve any purpose on a Tutorial type post.
C: Right MongoDB approach for a multigenomic database? by igor ♦ 8.0k
The benefit of MondoDB is that it's schema-less, but that is also its flaw. You can store anythin...
C: Ideas on how to evaluate genomic coordinates remapping tools? by juliette • 20
I do have the genomes in fasta files as well, I was just specifying what data I'm working on. Thi...

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