User: Sara
Sara • 90
- 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
... 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
Sara • 90
0
votes
0
answers
58
views
0
answers
... @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
Sara • 90
1
vote
0
answers
58
views
0
answers
... 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? ...
written 3 days ago by
Sara • 90
0
votes
0
answers
59
views
0
answers
... 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? ...
written 11 days ago by
Sara • 90
• updated
11 days ago by
Carambakaracho • 2.2k
0
votes
0
answers
74
views
0
answers
... 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 ? ...
written 15 days ago by
Sara • 90
• updated
15 days ago by
Pierre Lindenbaum ♦ 129k
1
vote
1
answer
101
views
1
answer
... 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 ...
0
votes
0
answers
128
views
0
answers
... 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? ...
written 3 months ago by
Sara • 90
• updated
3 months ago by
Pierre Lindenbaum ♦ 129k
0
votes
1
answer
61
views
1
answers
... @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
Sara • 90
0
votes
2
answers
141
views
2
answers
... 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. ...
written 3 months ago by
Sara • 90
• updated
3 months ago by
Devon Ryan ♦ 95k
0
votes
2
answers
162
views
2
answers
... 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 ...
written 4 months ago by
Sara • 90
• updated
4 months ago by
German.M.Demidov • 1.6k
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
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