User: dolevrahat

gravatar for dolevrahat
dolevrahat30
Reputation:
30
Status:
New User
Location:
Israel
Last seen:
7 months, 2 weeks ago
Joined:
6 years, 2 months ago
Email:
d*********@gmail.com

about me

Posts by dolevrahat

<prev • 30 results • page 1 of 3 • next >
0
votes
0
answers
208
views
0
answers
TCGA gene models and exon/isoform level expression data
... Hello I have downloaded mRNA expression data from TCGA-BLCA using TCGAbiolinks. I noticed that the expression quantification (FPKM/counts) are given at the gene level. I have two questions it this respect: 1. How can I tell exactly which exons are included in the gene models whose expression leve ...
tcgabiolinks gene models tcga rna-seq written 8 months ago by dolevrahat30
0
votes
0
answers
526
views
0
answers
Interpreting pairing probablities from RNAfold
... Hello I am trying to use RNAfold to predict the probability of each base in a mRNA is paired (with any base). I know I can extract the pairing probabilities for a base pair i,j from the dotplot PostScript file returned by RNAfold. Now I wonder if I can get the probability P(i) that the *ith* base ...
prediction secondary structure rnafold written 2.1 years ago by dolevrahat30
1
vote
1
answer
949
views
1
answers
Comment: C: Can I use different versions of dbsnp for variant calling using GATK and variant
... My question was if I can use different dbSNP files in the **variant calling** versus the **annotation** step, not between BQSR and the variant calling. The reason that I want to use different files in these steps is that for the variant calling I want to stick to the dbSNP vcf files provided by GATK ...
written 2.1 years ago by dolevrahat30
6
votes
1
answer
949
views
1
answer
Can I use different versions of dbsnp for variant calling using GATK and variant annotation?
... Hello I am using the GATK pipeline to do variant calling from human patients. For the purpose of tools in the GATK pipeline that require a list of known sites (e.g. BaseCallibrator) I am using the b37 dbSNP versuon 137 vcf available from the GATK resource bundle. Following variant calling I am an ...
variant calling gatk dbsnp variant annotation written 2.1 years ago by dolevrahat30 • updated 2.1 years ago by finswimmer13k
1
vote
1
answer
3.0k
views
1
answer
Difference in allele count between ExAC and gnomad exomes
... Hello I have recently queried the allele count for some variants using both gnomAD and ExAC. I found that for some variants, the allele count was much greater in ExAC then in gnomAD genomes. For example, for the variant chr13:25670851:A:G (hg19 coordinates) [ExAC][1] reports 194 occurrences, while ...
exome exac gnomad written 2.2 years ago by dolevrahat30 • updated 2.2 years ago by Kevin Blighe60k
0
votes
0
answers
910
views
0
answers
Comment: C: Filter low quality tiles from fastq files downloaded from SRA
... From the SRA, using fastq-dump ...
written 2.3 years ago by dolevrahat30
0
votes
0
answers
910
views
0
answers
Comment: C: Filter low quality tiles from fastq files downloaded from SRA
... I'm not I understand why. This is an example for a read ID from the file: SRR1976450.3 HWI-ST640:627:D26AFACXX:3:1101:1995:2149 As far I understand the sequence 3:1101:1995:2149 correspond to the flowcell lane,tile and X and Y coordinates within the tile. So it appear the information is there. ...
written 2.3 years ago by dolevrahat30
0
votes
0
answers
910
views
0
answers
Filter low quality tiles from fastq files downloaded from SRA
... Hello I am looking for a way to filter low quaility tiles from fastq files downloaded from SRA. I am aware that BBMap has a module called [FilterByTile][1] that does exactly that. However the developer state that "Renamed reads **(such as those in the SRA)** probably won’t work." Can anyone recom ...
quality filtering fastq sra written 2.3 years ago by dolevrahat30 • updated 2.2 years ago by Biostar ♦♦ 20
0
votes
2
answers
1.5k
views
2
answers
Comment: C: Summer internship in bioinfromatics - timing and visa issues
... Thanks! As I said I'm completely open to this idea. Do you have any recommendations where to look for comapnies in Europe or in Canada that might be offering internsips? ...
written 3.5 years ago by dolevrahat30
2
votes
2
answers
1.5k
views
2
answers
Forum: Summer internship in bioinfromatics - timing and visa issues
... Hello I am an Israeli M.Sc. bioinformatics student. I am planning to submit my thesis and finish all other obligations related to the Master's degree in the coming 4-6 months, and am currently considering a summer internship in the industry in the U.S. (I'm open to internships in other countries ...
forum internship written 3.5 years ago by dolevrahat30 • updated 3.5 years ago by Michael Dondrup47k

Latest awards to dolevrahat

Popular Question 11 months ago, created a question with more than 1,000 views. For Gene symbol disambiguties when match different gene symbol lists.
Popular Question 11 months ago, created a question with more than 1,000 views. For 3'UTR sequence for whole transcriptomes from biomart
Popular Question 11 months ago, created a question with more than 1,000 views. For command not found error when runing bismark modules with cluster flow
Popular Question 16 months ago, created a question with more than 1,000 views. For 3'UTR sequence for whole transcriptomes from biomart
Popular Question 16 months ago, created a question with more than 1,000 views. For command not found error when runing bismark modules with cluster flow
Popular Question 23 months ago, created a question with more than 1,000 views. For 3'UTR sequence for whole transcriptomes from biomart
Popular Question 23 months ago, created a question with more than 1,000 views. For command not found error when runing bismark modules with cluster flow
Popular Question 2.2 years ago, created a question with more than 1,000 views. For 3'UTR sequence for whole transcriptomes from biomart
Popular Question 2.4 years ago, created a question with more than 1,000 views. For 3'UTR sequence for whole transcriptomes from biomart
Popular Question 2.9 years ago, created a question with more than 1,000 views. For 3'UTR sequence for whole transcriptomes from biomart
Popular Question 3.5 years ago, created a question with more than 1,000 views. For 3'UTR sequence for whole transcriptomes from biomart
Popular Question 3.5 years ago, created a question with more than 1,000 views. For parallel fastQC computation
Popular Question 4.0 years ago, created a question with more than 1,000 views. For parallel fastQC computation
Scholar 4.1 years ago, created an answer that has been accepted. For A: Matrix index error when using dnet package to calculate semantic similarity of g

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1174 users visited in the last hour