User: David_emir

gravatar for David_emir
David_emir370
Reputation:
370
Status:
Trusted
Location:
India
Last seen:
13 hours ago
Joined:
6 years, 7 months ago
Email:
a************@gmail.com

about me

Posts by David_emir

<prev • 155 results • page 1 of 16 • next >
0
votes
1
answer
84
views
1
answer
Cancer driver mutations Identification from VCFs
... Hi All, I have merged.VCF(Around 45) file of a particular type of brain tumor sequenced from around ~45 patients. I have received only VCF files from the vendor and I don't have any .bam or .fasta/q files available. So my question is, can I apply any method/s or can I use any tool/s on the .vcf fil ...
vcf mcf driver mutation cancer written 5 days ago by David_emir370 • updated 4 days ago by Collin700
1
vote
2
answers
65
views
2
answers
Changing Sample Names in Merged VCF file
... Hi All, I have merged about 36 .vcf tumor Files into one single merged .vcf file. Now the problem is the vendor has given the .vcf file name as the R1_XXX_T_1.vcf and sample Name in vcf as Tumor, Likewise, all sample Names in .vcf is given as Tumor. My question is, can I change the sample name in m ...
vcf sample written 6 days ago by David_emir370 • updated 6 days ago by finswimmer13k
0
votes
2
answers
137
views
2
answers
Comment: C: Single cell Expression Analysis
... I meant Multiple patients data in single-cell gene expression analysis. Should we treat each sample individually ? does that make sense? Sorry, I might be wrong, but somewhere I fail to understand this. ...
written 19 days ago by David_emir370
4
votes
2
answers
137
views
6 follow
2
answers
Single cell Expression Analysis
... Hi All, I have 6,000 single-cell expression counts from 49 head and neck squamous cell carcinoma patients (20,000 Genes * 6000 cells /per sample). My question is how to conduct a differential expression of these samples, should I average (Merge) these samples to get a Raw count matrix or how to go ...
single cell rna seq written 19 days ago by David_emir370 • updated 18 days ago by jared.andrews074.9k
6
votes
2
answers
334
views
6 follow
2
answers
Validating Results from NMF Clustering & Consensus clustering
... Hi, I am running NMF/Consensus Clustering on my cancer samples and wanted it to cluster the samples into various subgroups, my question is how to conduct cluster assessment? Can I get P-value or something like that so that I can say my clustered samples are fine and validated? Regards, Dave ...
rna-seq validation written 7 months ago by David_emir370 • updated 7 months ago by anbarasu.la20
0
votes
1
answer
495
views
1
answers
Comment: C: What is the best pipeline for analyzing Non-invasive prenatal (NIPT) data?
... But, this is for fetal DNA quantification! Not exactly for identification of Trisomies. ...
written 9 months ago by David_emir370
1
vote
1
answer
1.1k
views
1
answers
Comment: C: Aligning Multiple paired end files together
... Thanks a lot for your help, i am able to sucessfully run BWA on my .fastq files. with following code, for f in $(ls *.fq_filtered | sed -e 's/_1.fq_filtered//' -e 's/_2.fq_filtered//' | sort -u) do bwa mem -t 20 hg19 ${f}_1.fq_filtered ${f}_2.fq_filtered > /path/to/be/saved/${f}.sam ...
written 9 months ago by David_emir370
0
votes
1
answer
1.1k
views
1
answers
Comment: C: Aligning Multiple paired end files together
... Thanks for the reply, i have added my script, please have a look ...
written 9 months ago by David_emir370
2
votes
1
answer
1.1k
views
1
answer
Aligning Multiple paired end files together
... Hi All, I have 72 paired end .fastq file for which i need to do Alignment using BWA. Since its a paired end data and my files are named as 1. sam_001_1.fastq 2. sam_001_2.fastq 3. sam_002_1.fastq 4. sam_002_2.fastq & so on Since its a paired end data i am not able to generate a single .s ...
assembly alignment bwa shell written 9 months ago by David_emir370
0
votes
1
answer
285
views
1
answers
Comment: C: NIPT for microdeletion and microduplication sydnromes
... Thanks a lot for your quick response. You mentioned about RAPIDr ... My question still remains valid, i did go through the git page. If you have missed, I'm looking for rapidr-plus package, I'm sure you will be having it, please share the link for all of us to download. Regards ...
written 10 months ago by David_emir370

Latest awards to David_emir

Popular Question 1 day ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 6 months ago, created a question with more than 1,000 views. For Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Popular Question 6 months ago, created a question with more than 1,000 views. For Quality control & Processing of RNA seq data
Popular Question 6 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 6 months ago, created a question with more than 1,000 views. For Genomic Matrix data from TCGA need to be analysied for Differential gene expression
Popular Question 6 months ago, created a question with more than 1,000 views. For What Types Of Analyses Are Typically Done After Snp Genotyping?
Popular Question 6 months ago, created a question with more than 1,000 views. For rna seq public databases
Popular Question 6 months ago, created a question with more than 1,000 views. For Error RNA-seq data, TOPHAT
Popular Question 6 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 7 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For rna seq public databases
Popular Question 8 months ago, created a question with more than 1,000 views. For Error RNA-seq data, TOPHAT
Popular Question 9 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 10 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 11 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 11 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 11 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 11 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Popular Question 13 months ago, created a question with more than 1,000 views. For Breast cancer TCGA data - DGE analysis
Scholar 13 months ago, created an answer that has been accepted. For A: Downloding only RNA-Seq Raw counts data from ICGC

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2020 users visited in the last hour