User: Bnf83

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Bnf83130
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Posts by Bnf83

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Comment: C: edgeR make contrast
... I totally agree with you! ...
written 5 months ago by Bnf83130
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Comment: C: edgeR make contrast
... No problem!!! I have around 100 breast cancer samples (primary). They performed RNA seq and then they clustered the samples identifying clusters (that here I called groups) of patients. Then They asked me the comparison I already explained. ...
written 5 months ago by Bnf83130
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Comment: C: edgeR make contrast
... I agree with you....anyway, suppose you have a gene "x" and you want to perform the DGE analysis on 10 samples of group A and 13 of group B. They asked me: DGA on A versus B plus A itself, i.e. if the expression of x in A is 40 and in B is 20, in A+B is 60, Finally the DGE will be 40 vs 60. Although ...
written 5 months ago by Bnf83130
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Comment: C: edgeR make contrast
... Unfortunately they do not receive a treatment or a specific condition and for this reason it seems strange a requirement of this type to me. Anyway: I think they would like the relative expression value of A, i.e. a sort of delta of A over A+B. I cannot figure out the rationale. ...
written 5 months ago by Bnf83130
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edgeR make contrast
... Hi guys, I'm dealing with a unusual analytical requirement: I'm performing differential gene expression of some human samples. I have neither controls nor replicates. The samples are grouped into two groups, let's say: A and B. Now I have to compare A vs B+A. Normally I compare A vs B. Never hap ...
contrasts rna-seq edger written 5 months ago by Bnf83130 • updated 5 months ago by i.sudbery5.0k
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From coverageBed to a list of reads per genes
... Hi guys, I'm analysing acChipSeq data. I performed all the steps of a canonical best practice pipeline. The last step was the coverageBed. Now, since I would like to perform a differential analysis for example using edgeR I need to have a matrix in which rows are genes and columns are samples. The ...
chip-seq written 5 months ago by Bnf83130 • updated 5 months ago by rrbutleriii70
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Chip seq (ac) reads count per pick
... Hi guys I have to analyze chip seq acetylation data. I'm a newbie in the field. I followed the typical pipeline proposed in many tutorials, i.e. starting from the alignment until the Macs peak calling. Now I have .merged.bed files that contain the merged picks (this was done using mergeBed). Now my ...
chip-seq written 5 months ago by Bnf83130 • updated 5 months ago by Pierre Lindenbaum121k
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Comment: C: Loop over .sai files coupled with .fastq.gz
... I'm working on a computer cluster ...
written 5 months ago by Bnf83130
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Comment: C: Loop over .sai files coupled with .fastq.gz
... Unfortunately parallel is not supported. I checked now :-( ...
written 5 months ago by Bnf83130
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Comment: C: Loop over .sai files coupled with .fastq.gz
... Dear Ram, I would like just to perform this: bwa sampe > for the full list of "paired" *.sai, *.fastq.gz files. ...
written 5 months ago by Bnf83130

Latest awards to Bnf83

Supporter 5 months ago, voted at least 25 times.
Great Question 2.0 years ago, created a question with more than 5,000 views. For How to define the gene length for RPKM calculation
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Are indel realignment and base recalibration necessary for RNAseq data?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For bedtools multicov not running
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How to define the gene length for RPKM calculation
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Inconsistencies between RNA Seq and PCR
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Gene level RNA seq expression measure
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Negative day values for Survival Analysis
Student 2.0 years ago, asked a question with at least 3 up-votes. For Inconsistencies between RNA Seq and PCR
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to define the gene length for RPKM calculation

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