User: Sara

gravatar for Sara
Sara90
Reputation:
90
Status:
Trusted
Location:
Last seen:
2 days, 21 hours ago
Joined:
3 years, 11 months ago
Email:
a***********@yahoo.com

Posts by Sara

<prev • 67 results • page 1 of 7 • next >
0
votes
0
answers
58
views
0
answers
Comment: C: how can I find the download link for a famous dataset
... the 1st pipeline is based on GATK and the 2nd one is based on DRAGEN. and the technology is Illumina. ...
written 2 days ago by Sara90
0
votes
0
answers
58
views
0
answers
Comment: C: how can I find the download link for a famous dataset
... @WouterDeCoster : well. I have a pipeline and trying to validate the pipeline. that is why I want to get this dataset and VCF file and use it for benchmarking. is that answer your question? ...
written 2 days ago by Sara90
1
vote
0
answers
58
views
0
answers
how can I find the download link for a famous dataset
... I am looking for both `fastq` and `vcf` file of this dataset : `NA12878`. I found this lind: https://www.internationalgenome.org/data-portal/sample/NA12878 but it is not clear which file belongs `NA12878`. can you help me to find `fastq` and `vcf` file for `NA12878` sample? ...
sequencing written 3 days ago by Sara90
0
votes
0
answers
59
views
0
answers
identifying the command for creating VCF file
... I have some `VCF` files. is it possible to find the command with which the `VCF` files are created? I know for alignment we can use `samtools` to find the alignment command. is there such tool for the `VCF` file? ...
snp written 11 days ago by Sara90 • updated 11 days ago by Carambakaracho2.2k
0
votes
0
answers
74
views
0
answers
evaluate the quality of VCF files for CNVs
... I have build a pipeline for `CNV` analysis of `WGS` data and trying to evaluate it. is there any way to evaluate the quality of resulting `VCF` files ? ...
genome sequencing written 15 days ago by Sara90 • updated 15 days ago by Pierre Lindenbaum129k
1
vote
1
answer
101
views
1
answer
correct order of cut off and normalization in RNAseq data
... I am a bit confused about applying cut off and normalization. for my RNAseq data I have raw counts, cpm and FPKM. I have 2 Scenarios to apply cut off: 1- using cpm: applying cut off and then normalized the raw counts (the normalized data would be cpm) 2- using FPKM: normalizing the raw coun ...
rna-seq written 7 weeks ago by Sara90 • updated 7 weeks ago by ATpoint36k
0
votes
0
answers
128
views
0
answers
CIBERSORT input file format
... I have RNAseq data and their count table. now I would like to use CIBERSORT https://cibersort.stanford.edu/ but it is not clear what the format of its input is. do you guys know what the CIBERSORT input file format is? ...
cibersort rna-seq written 3 months ago by Sara90 • updated 3 months ago by Pierre Lindenbaum129k
0
votes
1
answer
61
views
1
answers
Comment: C: quality control method for technical problem
... @ATpoint: Thanks for your answer. what do you mean by "quantify samples against the transcriptome"? do you mean align against transcriptome? ...
written 3 months ago by Sara90
0
votes
2
answers
141
views
2
answers
legal issues about running the analysis on the cloud
... I have 60 WES data and trying to do CNV analysis. if I run the tool locally it would take me a lot of time. so the solution that I thought about was using one of the famous clouds. but since my WES data is from patients I am wondering is this legal to run the analysis on clouds. ...
next-gen written 3 months ago by Sara90 • updated 3 months ago by Devon Ryan95k
0
votes
2
answers
162
views
2
answers
tool for the new protocol of WES for CNV detection
... to identify `CNVs` using `WES` data, I am trying to use WES data from a new protocol of `Agilent Whole Exon V7 + CNV backbone` which has additional regions added to the panel which is supposed to enable `CNV` for many known `CNV` regions. for this analysis I have used `GATK` for the old protocols b ...
next-gen written 4 months ago by Sara90 • updated 4 months ago by German.M.Demidov1.6k

Latest awards to Sara

Popular Question 12 weeks ago, created a question with more than 1,000 views. For frequency of each nucleotide at each position in sequence
Popular Question 3 months ago, created a question with more than 1,000 views. For frequency of each nucleotide at each position in sequence
Popular Question 7 months ago, created a question with more than 1,000 views. For DE analysis using single cell RNA-seq data
Popular Question 8 months ago, created a question with more than 1,000 views. For DE analysis using single cell RNA-seq data
Popular Question 8 months ago, created a question with more than 1,000 views. For M6A-seq and narrowpeak file
Popular Question 10 months ago, created a question with more than 1,000 views. For M6A-seq and narrowpeak file
Popular Question 19 months ago, created a question with more than 1,000 views. For identification of adapters from fastq file.
Popular Question 19 months ago, created a question with more than 1,000 views. For Isolating reads from specific region from bam file
Popular Question 19 months ago, created a question with more than 1,000 views. For how to visualize the RNAseq data on IGV
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Isolating reads from specific region from bam file
Popular Question 2.1 years ago, created a question with more than 1,000 views. For filtering genes out from bam file using samtools
Popular Question 2.1 years ago, created a question with more than 1,000 views. For error in macs2 usage

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 664 users visited in the last hour