User: star

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star190
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Posts by star

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Comment: C: why the TPM value is not same?
... I want to divide RPK per-sample RPK based on the below explanation: 1) Divide the read counts by the length of each gene in kilobases. This gives you reads per kilobase (RPK). 2) Count up all the RPK values in a sample and divide this number by 1,000,000. This is your “per million” scaling factor. ...
written 2 days ago by star190
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Comment: C: why the TPM value is not same?
... Thanks for your reply! Yes, I have removed it and Edited the cod now. In my cod I just used transpose : `TPM <- t(t(RPK)*1e6 / colSums(RPK))` and it looks work. but I don`t know what exactly happens after two times transposing? ...
written 2 days ago by star190
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why the TPM value is not same?
... I would like to do normalizing on my data using `TPM` methods like what explained https://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/ > TPM is very similar to RPKM and FPKM. The only difference is the order of operations. Here’s how you calculate TPM: > 1. Divide the read counts ...
R tpm normalizing edger rpkm written 2 days ago by star190 • updated 2 days ago by RamRS25k
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How to determine low and high variable row and column in a table?
... I have a big table, its rows are genomic coordinates and columns are the genomic features (like below). I would like to separate rows and columns based on the variability, I have tried to use some basic statistics like below codes, but I like to know is it the right way or is there an alternative (s ...
biostatistics methematics basic_statistics written 9 weeks ago by star190 • updated 7 weeks ago by Biostar ♦♦ 20
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How extract data from gnomAD for some genes?
... I like to extract variant details about some genes from gnomAD 'https://gnomad.broadinstitute.org/', but I don`t want to do it by hand. I would like to know, is there any way to extract it by command line for below genes? Table A: RFPL3 RGMA RGS11 RHOT1 RIPOR1 RIPOR3 R ...
data gnomad variants written 12 weeks ago by star190
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How draw Phylogeny tree using genotype file?
... I like to draw a phylogenetic tree for some samples based on SNP regions and genotype for each sample, I used 'SNPhylo' but it couldn`t help me because I only have 90 SNP regions and I got error based on 'SNPhylo'. I would like to know is there any way to draw a nice tree based on the data that I ha ...
phylogenic_tree R tree phylogenetic written 3 months ago by star190 • updated 3 months ago by YJ0
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Change color using colRow only for some rows in heatmap?
... I draw a heatmap using below command: but I want to color some rows in a different color (like red) in the heatmap e.g. only `ABCB5` and `MAD1L1` Data: gene.ID name A B ENSG00000002822 MAD1L1 0.00 0.01818182 ENSG00000007264 MATK 1.00 0.00000000 ENSG00000004846 ...
R heatmap written 3 months ago by star190
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Not call some variants in some populations?
... I have three VCF files from three populations where I merged all their SNPs together. For some variants, there are genotypes in all population but not for all regions, so I got 'NA', I like to know what does it mean? means: no variant call for this region in samples with 'NA' or can I consider 'NA' ...
vcf variantion written 3 months ago by star190 • updated 3 months ago by bari.ballew190
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Comment: C: why there is 0/0 genotyp in VCF file?
... We don`t get ./. genotype, if there is low Q mapping? ...
written 4 months ago by star190
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Comment: C: why there is 0/0 genotyp in VCF file?
... I guess it is only one sample. here is the header of VCF: ##GATKCommandLine.HaplotypeCaller= ...
written 4 months ago by star190

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