User: b.bearmi

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b.bearmi0
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Posts by b.bearmi

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Comment: A: How to annotate gene list using enrichr?
... not all the genes have annotated functions? Can you give an example of what enrichr has skipped? ...
written 11 weeks ago by b.bearmi0
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Comment: C: Interpreting allele values in VFC file
... Unless you are dealing with bacteria, you would have two copies of the same gene (plants - could be more, see "ploidy") 0/0 == G | G (G in copy one and G in copy 2, thinking humans: "one from mum and one from dad", unless you are studying something like X chromosome, then only females will have two ...
written 11 weeks ago by b.bearmi0
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Answer: A: mutate function dropping row names in r
... Can you include a short reproducible example of how your data looks like? If your row order (and number of rows) does not change you could just reassign row names from your `death` object ...
written 11 weeks ago by b.bearmi0
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Answer: A: Interpreting allele values in VFC file
... 0/0, 0/1, 1/1 refer to the genotype, a reference base called in a position would be 0/0, an alternative in one copy (presuming diploid) would be 0/1 and substitution in both alleles 1/1. Sometimes an alternative is called but the ratio between alternative and reference is less than 0.5 (either seque ...
written 11 weeks ago by b.bearmi0
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Answer: A: Definition of an isoform switching?
... In eukaryotes, genes don't have a continuous open reading frame, from start to stop codons, instead, they have exons (protein-coding bits) and introns (non-coding bits). After mRNA is transcribed, introns are spliced out of it. Cut sites on the initial mRNA are called splice sites. Some genes will h ...
written 11 weeks ago by b.bearmi0
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Comment: C: How to determine fibroblast contamination by expression profile
... I can certainly find some fibroblast-specific markers, based on this ResearchGate https://tinyurl.com/y77hg4zs discussion, they would be FSP1, collagens (I, III) - COL1A2; COL3A1, Thymic stromal lymphopoietin (TSLP) and Vimentin - VIM. Data is mostly open source, not every expression data is publish ...
written 13 months ago by b.bearmi0
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Comment: C: What is the best way to merge multiple fasta files containing contigs?
... If you want to merge overlapping sequences into one, try a scaffolding software, like sspace or soap-denovo. If you only want them in the same fasta file, then `cat`, like @ATpoint and @Asaf just said ...
written 13 months ago by b.bearmi0
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Comment: C: DGElist Ensemble ID recognized as NA values
... it is a bit hard to understand how your R object looks, can you try to reformat your question? when getting errors about NAs in R it is often about values *missing* from the input, not the format of them (unless it expects a numerical and gets a character) ...
written 13 months ago by b.bearmi0
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Answer: A: extract sample DP values from VCF
... cat file.vcf | awk -F ":" '/1/ {print $2}' > DP.values.from.vcf.file ...
written 13 months ago by b.bearmi0
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How to determine fibroblast contamination by expression profile
... I've got a series of data for a certain tissue, a type of cancer). We suspect that when tissues were sampled (biopsy/surgery) we end up with a mixture of different tissues, so when we do the analysis, it is not just the target tissue + tumour cells, it will also have a significant proportion of fibr ...
expression-profile rna-seq written 13 months ago by b.bearmi0 • updated 11 months ago by Biostar ♦♦ 20

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