User: Shaurya Jauhari

Reputation:
40
Status:
New User
Location:
India
Website:
http://www.twitter.com...
Twitter:
shauryajauhari
Scholar ID:
Google Scholar Page
Last seen:
2 days, 3 hours ago
Joined:
4 years, 7 months ago
Email:
s*******@instem.res.in

about me

Posts by Shaurya Jauhari

<prev • 27 results • page 1 of 3 • next >
1
vote
0
answers
188
views
0
answers
Different reflections from the techincal replicates.
... An experimental instance (mock-treated) was analyzed to have 24 upregulated genes (significantly differentially expressed). The technical replicate had none, which is apparently unusual. Is it all good here computationally or something went wrong? Could the biological provenance be questioned? I am ...
rna-seq written 10 days ago by Shaurya Jauhari40
0
votes
1
answer
209
views
1
answer
From the revered Tuxedo Suite for NGS data analysis, under what circumstances could the usage of Cuffmerge be thwarted?
... In a scenario where we are to compare paired-end RNA-Seq data from an instance of technical replicate, my understanding is that the Cufflinks output (pointedly transcripts.gtf) from each condition (mock-treated) will represent specific reads; until they are merged together to actually superimpose an ...
ngs data analysis rna-seq cuffmerge written 11 days ago by Shaurya Jauhari40 • updated 11 days ago by colindaven260
0
votes
0
answers
212
views
0
answers
Comment: C: Trimming Overrepresented Sequences in paired-end RNA-Seq data, as underlined by
... Thank you for your reply. Contrarily, is it also usual to have no overrepresented sequences at all. ...
written 13 days ago by Shaurya Jauhari40
2
votes
0
answers
212
views
0
answers
Trimming Overrepresented Sequences in paired-end RNA-Seq data, as underlined by FastQC.
... I am analyzing a RNA-Seq paired end sequence data. I have used cutadapt before to trim overrepresented sequences as derived from a fastqc report. However, this time around there is a slight twist in application. One of the reads I4_R1.fastq has the following attribute, >>Overrepresented ...
paired-end rna-seq fastqc written 14 days ago by Shaurya Jauhari40 • updated 14 days ago by genomax32k
1
vote
0
answers
148
views
0
answers
Cuffdiff output file gene_exp.diff has "no" for all listed genes under "significant" head.
... In context to the aforementioned statement, is that to say that my analysis is egregious hitherto. ...
cuffdiff rna-seq written 5 weeks ago by Shaurya Jauhari40
2
votes
1
answer
160
views
1
answer
Can't we proceed with a SAM file for downstream RNA-Seq data analysis?
... I'm aware that BAM file is easy to handle in terms of disk usage. If hypothetically, I register no shortage of processing power and memory, can I proceed with a SAM file for gene alignment and differential expression analysis? The due course would be different, but what would that be now? ...
sam file rna-seq data bam file written 6 weeks ago by Shaurya Jauhari40 • updated 6 weeks ago by jmzeng131420
7
votes
1
answer
243
views
5 follow
1
answer
Why does RNA sequencing data has Thymine as opposed to Uracil? Theoretically, it shouldn't be.
... As per definition, RNA has a quarternary composition of A,C,U,G. The RNA- sequencing data that is outputted from the next generation sequencing experiments still holds a T (from DNA) and not U. Why does the Uracil base has to be disengaged here? ...
rna-seq written 7 weeks ago by Shaurya Jauhari40 • updated 7 weeks ago by mark.ziemann870
0
votes
0
answers
1.5k
views
0
answers
Comment: C: SVM for classified gene expression data
... Thank you Dr. Heriche for the support. I'll take it from here. ...
written 18 months ago by Shaurya Jauhari40
0
votes
0
answers
1.5k
views
0
answers
Comment: C: SVM for classified gene expression data
... The following code finally worked: > library(e1071) > temp <- WorkFinalPDEG > temp$ID_REF <- NULL > temp <- log2(temp) > temp <- t(temp) > y <- c(rep(1,6),rep(-1,6)) > d <- data.frame(x=temp,y=as.factor(y)) > svmfit <- svm(y~., data=d, kernel="linear", c ...
written 18 months ago by Shaurya Jauhari40
0
votes
0
answers
1.5k
views
0
answers
Comment: C: SVM for classified gene expression data
... I tried again. Still shows an error. > library(e1071) > temp <- WorkFinalPDEG > temp$ID_REF <- NULL > temp <- log2(temp) > temp <- t(temp) > d <- data.frame(temp) > colnames(d)<- WorkFinalPDEG$ID_REF > labels<-as.factor(c(rep("normal",6),rep("tumor",6)) ...
written 18 months ago by Shaurya Jauhari40

Latest awards to Shaurya Jauhari

Popular Question 18 months ago, created a question with more than 1,000 views. For SVM for classified gene expression data

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1361 users visited in the last hour