User: Bnf83

gravatar for Bnf83
Bnf83150
Reputation:
150
Status:
Trusted
Location:
Last seen:
1 year, 2 months ago
Joined:
5 years, 10 months ago
Email:
e*******@campus.unimib.it

Posts by Bnf83

<prev • 40 results • page 1 of 4 • next >
0
votes
1
answer
940
views
1
answers
Comment: C: edgeR make contrast
... I totally agree with you! ...
written 15 months ago by Bnf83150
0
votes
1
answer
940
views
1
answers
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 15 months ago by Bnf83150
0
votes
1
answer
940
views
1
answers
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 15 months ago by Bnf83150
0
votes
1
answer
940
views
1
answers
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 15 months ago by Bnf83150
10
votes
1
answer
940
views
7 follow
1
answer
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 15 months ago by Bnf83150 • updated 15 months ago by i.sudbery7.7k
2
votes
1
answer
375
views
1
answer
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 15 months ago by Bnf83150 • updated 15 months ago by rrbutleriii70
2
votes
0
answers
320
views
0
answers
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 15 months ago by Bnf83150 • updated 15 months ago by Pierre Lindenbaum128k
0
votes
1
answer
469
views
1
answers
Comment: C: Loop over .sai files coupled with .fastq.gz
... I'm working on a computer cluster ...
written 16 months ago by Bnf83150
0
votes
1
answer
469
views
1
answers
Comment: C: Loop over .sai files coupled with .fastq.gz
... Unfortunately parallel is not supported. I checked now :-( ...
written 16 months ago by Bnf83150
0
votes
1
answer
469
views
1
answers
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 16 months ago by Bnf83150

Latest awards to Bnf83

Supporter 16 months ago, voted at least 25 times.
Great Question 2.9 years ago, created a question with more than 5,000 views. For How to define the gene length for RPKM calculation
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Are indel realignment and base recalibration necessary for RNAseq data?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For bedtools multicov not running
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to define the gene length for RPKM calculation
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Inconsistencies between RNA Seq and PCR
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Gene level RNA seq expression measure
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Negative day values for Survival Analysis
Student 2.9 years ago, asked a question with at least 3 up-votes. For Inconsistencies between RNA Seq and PCR
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How to define the gene length for RPKM calculation

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1258 users visited in the last hour