User: gradstudentNew

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Posts by gradstudentNew

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Comment: C: Effect Allele Frequency in base summary statistics for PRSs calculation
... Do you mean 0.49 instead of 0.09? ...
written 4 days ago by gradstudentNew30
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Meta-analyzing DESeq2 output
... Hello, I was wondering what your thoughts were on meta-analyzing different datasets based on their test statistic or p-value from different DESeq2 outputs? Also, are there any differences with meta-analyzing between LRT and Wald output? I wasn't sure whether I should transform the test statistic fi ...
rnaseq deseq2 written 4 days ago by gradstudentNew30
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Comment: C: DESeq2 counts (inverse relationship)
... Thanks for the reply! Yes, these are biological replicates and the genomic region was deleted or introduced through CRISPR. There are other genes deleted within the region that show the expected trend (no expression for homozygous, decreased for heterozygous, and increased expression of duplication) ...
written 7 days ago by gradstudentNew30
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Comment: C: DESeq2 counts (inverse relationship)
... Thanks for the reply! Actually, this gene should've been deleted as well (I deleted an entire structural region via CRISPR and it was confirmed genetically too) . It is making me wonder whether there is off target mapping from STAR? ...
written 7 days ago by gradstudentNew30
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DESeq2 counts (inverse relationship)
... Hi there, I recently conducted an experiment where I deleted a region of the genome. I found that there was a weird trend where the homozygous deletion for certain genes had higher expression compared to wild type, heterozygous deletion as shown below. I was wondering what your thoughts on this may ...
counts rna-seq written 8 days ago by gradstudentNew30 • updated 8 days ago by Istvan Albert ♦♦ 82k
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Comment: C: Complex DESeq2 Model with different gene dosages
... Would I just do a venn diagram to look at overlap afterwards between the two cell types? ...
written 12 days ago by gradstudentNew30
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Comment: C: Complex DESeq2 Model with different gene dosages
... Apologies. Celltype is amongst either neurons or glia. Dosage refers to the number of copies of the allele. This is either 0 (homozygous deletion), 1 (heterozygous deletion), 2 (wildtype), 3 (duplication). RIN is the RNA integrity number yes. I've seen several papers putting RIN into their model so ...
written 12 days ago by gradstudentNew30
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Complex DESeq2 Model with different gene dosages
... Hi there, I am currently trying to design a statistical model for DESeq2 that encompasses what I'm looking for. Essentially, I have a double knockout, heterozygous knockout, wild type, and duplication for 2 cell lines. I put random RIN numbers for the sake of this example. Amongst each group, there ...
rnaseq genes deseq2 statistics written 12 days ago by gradstudentNew30
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Complicated Multi-factor Differential Expression
... Hello all. Merry Christmas and happy holidays! I am currently conducting a study and was hoping to get some advice on my model for differential expression. Currently, I have the following data: Sample || Sex || Age || TissueType || Individual || Diseased ID1 || Male || 70 | ...
rnaseq multifactor sleuth differential expression written 14 months ago by gradstudentNew30 • updated 13 months ago by Charles Warden7.6k
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Keeping both A1/A2 in PLINK for assoc/logistic output
... Hey guys, I was wondering if there's anyway to keep both A1 and A2 in PLINK for the logistic output? I used to merge my freq. output and assoc output. However, since I use HWE / MAF filters, it only applies to the logistic and the merging no longer works since they're not in order anymore. Any su ...
gwas plink written 18 months ago by gradstudentNew30 • updated 18 months ago by chrchang5236.5k

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Popular Question 10 months ago, created a question with more than 1,000 views. For Extracting certain columns from VCF file

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