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Comment: PCA plot (Suggestions Needed)
by
swbarnes2
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Cross posted here (including the code used to make up the counts):
https://support.bioconductor.org/p/9157911/#9157959
Comment: To get p-values for the TPM
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swbarnes2
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RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
Comment: How to trim transcripts using information from NCBI contamination screen report
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Lada
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i checked both of these programs (`bbduk` and `fastp`) and it seems they use reads as inputs (fastq formats)... how can I trim my transcrip…
Comment: AGeNT LocatIt
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barslmn
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He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
Comment: How to convert plink files to Hapmap Format
by
bk11
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This looks good. Please try with using `--allow-no-sex flag`
plink --bfile your_data_phenoUP --assoc --allow-no-sex --out your_data_ph…
Comment: How to convert plink files to Hapmap Format
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Sofia
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SC899359_PC75420_A05 SC899359_PC75420_A05 0 0 0 2
SC899360_PC75415_D01 SC899360_PC75415_D01 0 0 0 2
SC899361_PC75425_H05 SC899361_PC75425_H…
Comment: How to convert plink files to Hapmap Format
by
bk11
★
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Please show me a few lines of phenotype updated .fam file. You can do `head
your_data_phenoUP.fam` and paste result here. Please do not us…
Comment: GEMMA GWAS how to specify factor or numerical for covariates
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Sofia
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Hi, I don't have a solution to your question but I followed this tutorial and was helpful to me in my analysis https://youtu.be/NusV6duyvXs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
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Catalog file lists the genomes included. There seem to be 71365 unique items in field 2.
2 Bacteria WP_000018326.1 4459…
Comment: How to convert plink files to Hapmap Format
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Sofia
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yes sure !
![enter image description here][1]
[1]: /media/images/f0f94f6c-4387-4188-a1aa-19152a89
Answer: AGeNT LocatIt
by
Greg
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Give it more memory.
~10x more memory, or whatever you can give it,
I had samples that weren't even close to being done after 3.5 da…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
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Thanks! I've already tried looking through these files, I need release 83. I am trying to find this information in the .catalog file of the…
Answer: Is it possible to get a list of representative genomes from a past RefSeq releas
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GenoMax
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Possibly. You will need to know the RefSeq release version. Check in this directory: https://ftp.ncbi.nlm.nih.gov/refseq/release/release-ca…
Comment: How to convert plink files to Hapmap Format
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bk11
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Hey, can you please show me a few lines of your phenotype updated .fam file? I m seeing there are 7 columns in it, that might be the proble…
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jkim
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How much variance were explained by PC1 and PC2? It doesn't look like that the largest source of variation came from the genotype differenc…
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