User: Ron
Ron • 600
- Reputation:
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- United States
- Last seen:
- 4 weeks, 1 day ago
- Joined:
- 3 years, 7 months ago
- Email:
- r*********@yahoo.co.in
about me
Posts by Ron
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... Hi all,
I found Oncogenic viruses using VirusSeq (http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html )in some of the RNA-seq HUMAN samples.However I want to view the evidence of these virus reads in IGV.
Should I just align the human RNA-seq to virus genome ,get the bam using STAR and load the bam fi ...
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... Usually I use Junction Reads > 2 and Spanning Pairs > 1 for fusions with good support.
Although there could be novel fusions with only Junction Reads or only Spanning Pairs .
...
written 8 weeks ago by
Ron • 600
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... Hi all,
Is it possible to get MAplots when you only have foldchange and Expression values of the two samples of comparison(one vs one) ?
I don't have replicates.So i only have FPKMS from 2 samples and their log2FoldChange.I know I don't have statistical significance but I still would like to have M ...
written 10 weeks ago by
Ron • 600
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... Hi all,
I am doing mutation analysis on RNAseq using rnaseqmut ( https://github.com/davidliwei/rnaseqmut )
.Is there any way to annotate mutations with the actual motifs?
I want to look if some mutations lie in specific motifs of interest e.g. CCAUCG
Thanks,
Ron
...
written 3 months ago by
Ron • 600
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... VirusFinder: Software for Efficient and Accurate Detection of Viruses and Their Integration Sites in Host Genomes through Next Generation Sequencing Data
I came across this software and its easy to install compared to the others,and it gives good results.
e.g. I had some samples positive for viruse ...
written 4 months ago by
Ron • 600
0
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... Are you still working on getting LM22 signature? ...
written 4 months ago by
Ron • 600
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3
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584
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... Were you able to find the older version of Trinity? ...
written 4 months ago by
Ron • 600
0
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1
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409
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... Hi all,
I want to create Silhouette plots in R.
I have the code for that:
library (cluster)
library (vegan)
dis = vegdist(exp_matrix)
res = pam(dis,3) #choice of clustering algorithm
sil = silhouette (res$clustering,dis) # cluster vector
pdf('my_nice_plot.pdf')
plot( ...
written 4 months ago by
Ron • 600
• updated
4 months ago by
Mattias Aine • 410
0
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... You can get isoforms expression from Cufflinks in the isoforms.fpkm_tracking file. ...
written 5 months ago by
Ron • 600
0
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3
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Comment:
C: CAGE seq & RNA-seq
... I just want to use FANTOM data which has different cell types and do clustering analysis with regular RNAseq data based on Expression levels.Has anybody done this kind of analysis ?
I am not interested in the primary purpose served by CAGE,thats what I mean.Since FANTOM has multiple cell types Exp ...
written 5 months ago by
Ron • 600
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