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Recent Replies
Answer: Annotation comparison files on NCBI of gene assembly
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GenoMax
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> May I ask if there exist a documentation that explains this further?
There is a file that describes the specific categories: https://ftp…
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andres.firrincieli
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That paper (https://www.nature.com/articles/s41598-023-40799-x) conflates a taxonomic classifier (Kraken2) with a broader analysis platform…
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Attaching a screenshot for ready reference. Full size PDF linked above.
Posted as an issue to InferCNV already: https://github.com/broadin…
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> local SSDs are cheap and very fast
And keep in mind that they will wear out, especially if you are writing TB's of data regularly.
Comment: Strandedness issues in STAR quantification
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GenoMax
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Looks like you have already opened an issue on STAR repo: https://github.com/alexdobin/STAR/issues/2650
That was going to be the next sugg…
Comment: How to Remove Phasing Information from a VCF File?
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Mwangana
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How can I use bcftools +setGT to get genotypes without phase e.g. "|" or "/"?
For example, instead of 1|1 or 1/1, I would like to get 11
Answer: Two config files for one Snakemake file
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That is exactly what Snakemake is for.
You could create a `sample` variable at the top of a `config.yaml` file and loop over these samples…
Answer: Exome data analysis computing resources requirement query
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What others have said, but also
- whats your approx budget?
- Maybe if low budget you can get a long way by using local SSDs on works…
Comment: Strandedness issues in STAR quantification
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marek.gierlinski
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I tried STAR counting with an index created without GTF. The results are identical to those based on index created with GTF. Every single c…
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You can get some data from GDC portal: https://portal.gdc.cancer.gov/analysis_page?app= and https://portal.gdc.cancer.gov/analysis_page?app…
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Can I get TCGA somatic mutation vcf files or maf files
for MSI - H, MSI-L - MSS samples?
I mean open access without any special access…
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What kind of technology is this data from? If it is Parse tech data then you may need to use their pipeline that you can get from here: htt…
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> duplicated genes
What is the origin of those genes. Are they entries with same name in GTF but different chromosomal locations (e.g. cop…
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Yes, the y-axis is reasonable. ALthough the test for differences should come from DESeq, rather than from a wilcox in this case. With four …
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saruman
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Done. Thank you.
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