User: Lorenzo

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Lorenzo0
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Posts by Lorenzo

<prev • 19 results • page 2 of 2 • next >
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Analysis of RNA-seq data
... Hi to all, I have RNA-seq data from 31 tissues of 2 different individuals. My goal is to evaluate the expression of various genes of interest and to compare the expression level among these tissues. I read throughout a lot of papers and posts and I tried to set up my pipeline. I mean first of all a ...
rna-seq written 8 days ago by Lorenzo0 • updated 8 days ago by Istvan Albert ♦♦ 85k
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Normalization with deepTools
... Good morning, I'm doing RNA-seq analysis. I have .bam files coming from 31 different tissues. My goal is to normalize these data in order to obtain .bigwig files and compare them on IGV. Can I use bamCoverage (from deepTools) to do that? If yes, how can I do it? Thank you in advance for your time ...
rna-seq written 13 days ago by Lorenzo0 • updated 13 days ago by Friederike6.5k
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Comment: C: Suggestion for Differential Expression analysis
... Ok thank you actually I have the same type of tissues from another individual so I can do it to determine the biological relevance. Now I have to improve my skills on R to do it. Thank you again! ...
written 18 days ago by Lorenzo0
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Comment: C: Suggestion for Differential Expression analysis
... Ok thank you for your explanation. So to perform DEA it is necessary to have at least 2 replicates for each tissue? Is there a way to consider the different tissues like different replicates? I mean I have so many tissues and in my mind I'm not able to understand why it is not possible to perform DE ...
written 18 days ago by Lorenzo0
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Comment: C: Suggestion for Differential Expression analysis
... No it is a part of a big project and considering the fact that we have the reads coming from the transcriptome we decided to do that. ...
written 18 days ago by Lorenzo0
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Comment: C: Suggestion for Differential Expression analysis
... I posted the full colData because now I'm not using all tissues because I want to set my pipeline and see if it works on only 4 tissues. My first problem is here: > dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ Tissue) Note: levels of factors in the ...
written 19 days ago by Lorenzo0
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Comment: C: Suggestion for Differential Expression analysis
... Could you help me please? I'm a beginner in R and I'm encountering some problems. > library(DESeq2) > countData <- as.matrix(read.csv("gene_count_matrix.csv", row.names="gene_id")) > colData <- read.csv("Pheno_data.csv", row.names=1) > all(rownames(colData) %in% co ...
written 19 days ago by Lorenzo0
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Comment: C: Error in prepDE.py after StringTie quantification
... Thanks! Now it works. It was too easy. Thanks again!!! ...
written 20 days ago by Lorenzo0
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Error in prepDE.py after StringTie quantification
... Hello, I am doing RNA-seq analysis, using the pipeline suggested here ([http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq][1]). I utilized StringTie to map my reads, to assemble transcripts and to estimate transcript abundances. Reading throughout different posts I have decided to use ...
rna-seq written 20 days ago by Lorenzo0

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