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written 9 months ago by
venuraherath • 20
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Eli Korvigo • 150
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written 4.5 years ago by
Chris Cole • 680
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4.5 years ago by
dcnorris • 270
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Recent Replies
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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...
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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/
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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...
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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...
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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...
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C: Ideas on how to evaluate genomic coordinates remapping tools? by
igor ♦ 8.0k
Interesting. How would it work without chain files?
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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...
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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...
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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...
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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.
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igor ♦ 8.0k
The benefit of MondoDB is that it's schema-less, but that is also its flaw. You can store anythin...
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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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