User: Santosh Anand

gravatar for Santosh Anand
Santosh Anand3.7k
Reputation:
3,680
Status:
Trusted
Location:
Last seen:
10 minutes ago
Joined:
2 years, 5 months ago
Email:
s************@gmail.com

Posts by Santosh Anand

<prev • 568 results • page 1 of 57 • next >
1
vote
4
answers
154
views
4
answers
Answer: A: How to get PCA3 and PCA4 from Deseq2?
... Here is my version of plotPCA ## Modified plotPCA from DESeq2 package. Shows the Names of the Samples (the first col of SampleTable), and uses ggrepel pkg to plot them conveniently. # @SA 10.02.2017 library(genefilter) library(ggplot2) library(ggrepel) plotPCA.san < ...
written 2 days ago by Santosh Anand3.7k
0
votes
0
answers
149
views
0
answers
Comment: C: covert SAM to full length fasta
... what's wrong with the 2nd solution ? samtools bam2fq input.bam | seqtk seq -A - > output.fa I mean could be more clear about "aligning these sequences to single seq" ? ...
written 2 days ago by Santosh Anand3.7k
0
votes
1
answer
113
views
1
answers
Comment: C: How to know which samples are treated and untreated?
... Actually, I wanted to point out to OP two things by above reply. 1) You can always get the full information of samples from GEO page, as sometimes gleaning this info from publication is difficult and also 2) GEO page can serve as a cross-reference to check your metadata. > Do you know which par ...
written 3 days ago by Santosh Anand3.7k
3
votes
1
answer
76
views
1
answers
Answer: A: Interpretation of Overlapping p-value = 0 and Odss ratio = Inf
... What is that you did not understand? You are testing for the overlap between listA and listB. And your listA is a subset of listB (all the elements of listA are in listB). This means that the overlap between them is highly significant => p-value = 0 (actually it is a very small number rounded to ...
written 3 days ago by Santosh Anand3.7k
1
vote
1
answer
113
views
1
answers
Answer: A: How to know which samples are treated and untreated?
... There are Expression data from 290 primary colorectal cancers. Sample description is here https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333 Click on your GSM* to know more about them ...
written 4 days ago by Santosh Anand3.7k
0
votes
1
answer
112
views
1
answers
Comment: C: How to determine RNA-seq samples from dbGaP metadata
... Check the paper, you'll get the idea. "...Unique to capture transcriptomes is an overnight capture reaction (RNA-DNA hybridization) using exon-targeting RNA probes, followed by a washing step, and an additional set of PCR cycles..." ...
written 4 days ago by Santosh Anand3.7k
0
votes
1
answer
112
views
1
answers
Answer: A: How to determine RNA-seq samples from dbGaP metadata
... My guess is that the Exome related stuffs refer to Exome Capture RNAseq https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561495/ The key point is "degraded samples" where RNA cant be captured by usual ribo-zero or polyA (see paper above) This is also evident from the description of data types https ...
written 4 days ago by Santosh Anand3.7k
2
votes
1
answer
110
views
1
answers
Answer: A: gatk vqsr --recal-file error
... Probably the argument has been deleted as I could not find anything on the argument lists https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.3.0/org_broadinstitute_hellbender_tools_walkers_vqsr_VariantRecalibrator.php Also, there is a thread on GATK reg. this and you may also like ...
written 4 days ago by Santosh Anand3.7k
0
votes
0
answers
137
views
0
answers
Comment: C: Error when indexing a bcf file
... https://github.com/EBIvariation/vcf-validator ...
written 4 days ago by Santosh Anand3.7k
1
vote
2
answers
106
views
2
answers
Comment: C: Survival plot between low and high expression of gene
... As I said above, rpkm and normalized counts are measuring the same things - but in a different way. So if your choice of counts changes the result, you may dig deeper why it is happening by looking which samples are changing from high -> low group and why. There is no universal answer if rpkm is ...
written 4 days ago by Santosh Anand3.7k

Latest awards to Santosh Anand

Popular Question 2 days ago, created a question with more than 1,000 views. For chart title in plotly (R)
Teacher 3 days ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 4 days ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Scholar 4 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 4 days ago, created an answer that has been accepted. For A: How can we download all TSA and WGS from NCBI Trace by taxon programmatically?
Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: Can STAR work with compressed .gz FASTQ input?
Appreciated 10 days ago, created a post with more than 5 votes. For A: How to recover treated/control count from DESeq2 output
Scholar 10 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 4 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Appreciated 5 months ago, created a post with more than 5 votes. For A: How to recover treated/control count from DESeq2 output
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 7 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 7 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 10 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 10 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 11 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: read.table does not read in all rows!
Scholar 12 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1860 users visited in the last hour