User: itspilipineiro

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Malaga
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36 minutes ago
Joined:
8 months, 2 weeks ago
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i*************@gmail.com

Im a Health Engineering student doing an Artificial Intelligence master's degree and working on epigenetics

Posts by itspilipineiro

<prev • 11 results • page 1 of 2 • next >
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RNA-Seq AUTOMATIC workflows available/ make your own
... Hello, I am relatively new to RNA-Seq analysis, and Im wondering if people who do these kind of analysis have a workflow predefined or they just run trimming, mapping, quantification and DE analysis (for example) independently.. If there are workflows available, where can I find them? Or how could ...
rna-seq written 1 hour ago by itspilipineiro20
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Where can I find bisulfite sample data to practice trimming, mapping and methylation call? Im new in this field
... Hello, I am learning to analyze bisulfite reads analysis: trimming mapping and methylation calls Is there any data available for learning? Also, are trim galore and bismark the most used softwares or are there better alternatives? Any good websites I should look at for theory aswell? Thank you ve ...
bs-rna-seq methylation bisulfite written 1 hour ago by itspilipineiro20 • updated 47 minutes ago by Joseph Hughes2.4k
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Comment: C: Is it possible to find a human genome STAR index to not have to create it on my
... Thank you very much, that is a great solution. But im having a hard time finding the gtf annotation by chromosome: i believe i can get the fasta here: ttp://hgdownload.cse.ucsc.edu/downloads.html#human But no idea on where to find the .gtf to generate the index Any suggestions? ...
written 3 days ago by itspilipineiro20
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Comment: C: Is it possible to find a human genome STAR index to not have to create it on my
... EDIT: I know its better to generate our own indexes but this is a trial mapping so it's only for teaching purpose and i dont need to be exact ...
written 4 days ago by itspilipineiro20
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Is it possible to find a human genome STAR index to not have to create it on my laptop?
... Hello, I need to map human tumor reads to a reference genome and to do so I need to create the index in STAR. I would have to download the human genome and i dont have enough memory. Does star provide with common genome indexes already generated? Or is there another solution? Thank you ...
human genome star mapping rna-seq star idex written 4 days ago by itspilipineiro20 • updated 3 days ago by genomax40k
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Answer: A: How to plot a heat map for the top 30 differentially expressed genes.
... Compute the differential expression itself: dds <- DESeq(dds_7) RLog: rld <- rlog(dds, blind=F) Select the top genes topVarGenes <- head(order(-rowVars(assay(rld))),30) mat <- assay(rld)[ topVarGenes, ] mat <- mat - rowMeans(mat) pheatmap(mat) ...
written 8 months ago by itspilipineiro20
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What classifying or clustering tools should I apply for an exhaustive gene expression analysis?
... Hello, I am working on a project and I have already done a differential expression analysis (a simple pairwise comparison with DESeq2). I have 5 conditions: + infected with bacteria + infected with fly + not infected but exposed to bacteria + not infected but exposed to fly + untreated (NAIVE) F ...
gene R rna-seq written 8 months ago by itspilipineiro20
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Comment: C: Differential expression analysis 5 conditions 3 replicates each matrix counts
... Thanks Devon. I dont know what else should I be interested in or what els I could do .. (maybe something regarding time series?) Again, thank you ...
written 8 months ago by itspilipineiro20
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Comment: C: Differential expression analysis 5 conditions 3 replicates each matrix counts
... Hello, yes il explain better: Samples were taken at 2, 7, 14 and 21 days post infection. There are 5 conditions , and 3 plants (or biological replicates) for each condition. I decided to do a diferential expression analysis for each dpi independently with DESeq2, and I did the following : samp ...
written 8 months ago by itspilipineiro20
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Comment: C: Differential expression analysis 5 conditions 3 replicates each matrix counts
... Hello thank you so much, I was a little lost. So here is what I did once i got my counts matrix as cts. I dont know if the results I got are correct: I wanted to do many comparisons, I have 3 samples for each of 5 conditions: sampleTable<-data.frame(row.names=c("Bm14a","Bm14b","Bm14c","BTY1 ...
written 8 months ago by itspilipineiro20 • updated 8 months ago by Devon Ryan74k

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