User: sunil.mangalam

Reputation:
0
Status:
New User
Location:
United States
Last seen:
5 months, 1 week ago
Joined:
2 years, 2 months ago
Email:
s*************@gmail.com

Posts by sunil.mangalam

<prev • 9 results • page 1 of 1 • next >
0
votes
2
answers
659
views
2
answers
Comment: C: Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased da
... Yes, I agree... Actually I got confused with a comparison of a cuffdiff analysis with the STAR-FeatureCounts-DeSeq2 pipeline I did long back. At that time I interpreted it as an effect of the FPKM normalization, but perhaps it is more because cuffdiff is very conservative compared to DeSeq2. For wha ...
written 5 months ago by sunil.mangalam0
0
votes
2
answers
659
views
2
answers
Comment: C: Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased da
... Hi Michael,  I want to dig into this a bit. more. As you mentioned, there is some splicing info in 3' biased data, but the number of reads drops of precipitously as we move towards the 5' end of genes in my data set. When I use featureCounts, normalizing for gene length by FPKM/RPKM really screwed ...
written 5 months ago by sunil.mangalam0
0
votes
2
answers
659
views
2
answers
0
votes
2
answers
659
views
2
answers
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
... Hi, I wist to use tximport followed by DeSeq2 for differential expression analysis of RNA-Seq data quantified by Salmon (from fastq files). The libraries are 3' end biased  and have limited isoform level information (situation similar to that shown in Figure 1C of the Sonenson et al paper on the tx ...
deseq2 salmon tximport "tximport" written 5 months ago by sunil.mangalam0
0
votes
0
answers
550
views
0
answers
Monocle-strange differential expression results
... Hi, I did a pilot monocle analysis with 34 single cell samples.I am modeling  a branched pathway with a progenitor cell (n=5), giving rise to 3 mature cell types (n=9-11). I understand that it is hugely under powered, but on the plus side, the libraries are sequenced very deep (30-70 million reads ...
differential expression monocle written 22 months ago by sunil.mangalam0
1
vote
1
answer
491
views
1
answer
DeSeq help with PCA
... Hi,  I have some questions about PCA in DeSeq2. Is the PCA based on all genes in the input list or the subset of highly differentially expressed genes? If so, how can I extract this subset? I have 5 groups in my PCA with multiple replicates and extracting the subset of genes that drive the PCA resu ...
deseq2 pca written 2.1 years ago by sunil.mangalam0 • updated 2.1 years ago by Michael Love15k
0
votes
2
answers
2.9k
views
2
answers
Comment: C: Deseq2 rlog or 'regular' normalization?
... Thanks Michael, The behavior you describe is exactly what I see for many genes (14.2% in my dataset to be exact).I think there will be dropouts in many cases , for example when genes have a different intron/exon structure in the cell type we analyze  than what is in the gtf files we use for analysi ...
written 2.2 years ago by sunil.mangalam0
0
votes
2
answers
2.9k
views
2
answers
Answer: A: Deseq2 rlog or 'regular' normalization?
... Thanks a lot for for your reply, Simon. I want to do a principal component analysis, calculate Pearson's correlation coefficient between pairwise comparison of all samples, and a hierarchical clustering and heat map where I use only a subset of genes that pass a  differential expression cutoff (typ ...
written 2.2 years ago by sunil.mangalam0
0
votes
2
answers
2.9k
views
2
answers
Deseq2 rlog or 'regular' normalization?
... Hi,  I am facing some difficulties with data transformations of my single cell RNA-Seq data analyzed using DESeq2. This data set is different from typical RNA-Seq experiments.. For example, there is a subset of genes which will be present in one group and totally absent in the other, unlike typical ...

Latest awards to sunil.mangalam

Popular Question 22 months ago, created a question with more than 1,000 views. For Deseq2 rlog or 'regular' normalization?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 111 users visited in the last hour