User: reza.jabal

gravatar for reza.jabal
reza.jabal420
Reputation:
420
Status:
Trusted
Location:
New York, USA
Twitter:
mjabal
Last seen:
1 day, 10 hours ago
Joined:
5 years, 7 months ago
Email:
r*********@yahoo.co.uk

Posts by reza.jabal

<prev • 96 results • page 1 of 10 • next >
0
votes
1
answer
168
views
1
answers
Answer: A: How to calculate the conservation score of a gene
... There are a few well-established annotation software that accepts multiple input format and annotates your genes/variants with pathogenicity and conservation metrics from different methods/databases. If you're not familiar with command-line scripting, I recommend taking a look at [VEP][1] and [wAN ...
written 6 weeks ago by reza.jabal420
0
votes
1
answer
168
views
1
answers
Comment: C: How to calculate the conservation score of a gene
... What do you mean by calculation? Do you want to calculate conservation scores from scratch or you just want to annotate your gene list with pre-calculated conservation scores? There are multiple resources for pre-calculated conservation scores. Such as [`GERP`][1] and [`Phylop`][2] to name a few! ...
written 7 weeks ago by reza.jabal420
0
votes
0
answers
126
views
0
answers
Comment: C: Time series with biological replicates
... I second @rpolicastro answer regarding `negative binomial`. Also suggest `generalized mixed models` for the differences in patients. You can model the heterogeneity as a random effect in your model. ...
written 7 weeks ago by reza.jabal420
2
votes
1
answer
118
views
1
answers
Answer: A: Understanding SNP variant output
... In re-sequencing applications such as Whole-exome/Genome sequencing (WES/WGS), we align the sequenced contigs against a [reference genome][1] which is perceived as ground truth for the correct letter at each position. The REF represents the reference allele, and ALT represent anything else that is n ...
written 7 weeks ago by reza.jabal420
2
votes
1
answer
215
views
1
answers
Answer: A: What is a suitable LD threshold for LD pruning of snp data?
... The choice of optimal r^2 threshold for LD pruning is highly dependent on the population history of your study subjects. Despite D' that is purely a measure of the non-random association of alleles at two or more loci, r^2 values are informed by allele frequencies as well. For example for two polymo ...
written 9 weeks ago by reza.jabal420
0
votes
0
answers
369
views
0
answers
Comment: C: extract genes and functions +/-50kb around a SNP
... Hi Pierre, Would you please update your answer to reflect the current dbSNP version? ...
written 8 months ago by reza.jabal420
0
votes
0
answers
436
views
0
answers
Comment: C: Filtering multiple single person structural variant VCF files by type of SV
... So `grep` should work absolutely fine with your `vcf`. Lets assume your multi-call VCF file is: `output.vcf` cat SV.list | while read i do; grep $i output.vcf > ${i}.sub.vcf done should do the trick! Also have a look at SnpEff "Primary variant annotation and quality contro ...
written 10 months ago by reza.jabal420
1
vote
0
answers
436
views
0
answers
Comment: C: Filtering multiple single person structural variant VCF files by type of SV
... I see! I was under impression that you have a multi-call vcf file containing all variants across your samples. In that case you need to generate a multi-call vcf. You can use either vcftools or GATK but I recommend GATK: https://gatkforums.broadinstitute.org/gatk/discussion/53/combining-variants-fro ...
written 10 months ago by reza.jabal420
0
votes
0
answers
243
views
0
answers
Comment: C: Fastq to VCF pipeline configuration for low coverage data
... Your heterozygous calls are only valid for loci that reads overlap and with single-pass sequencing depth, you have no reliable source to judge about heterozygote loci. If you're working with the human genome, you can use https://gencove.com/ for imputation, but I am not sure whether 1x depth is suff ...
written 11 months ago by reza.jabal420
1
vote
0
answers
436
views
0
answers
Comment: C: Filtering multiple single person structural variant VCF files by type of SV
... Make a list file with Manta codes: echo "MantaINS" >> SV.list echo "MantaINV" >> SV.list echo "MantaDEL" >> SV.list echo "MantaBND" >> SV.list echo "MantaDUP" >> SV.list echo "Canvas:REF" >> SV.list ... Then do, cat SV.list | whi ...
written 11 months ago by reza.jabal420

Latest awards to reza.jabal

Scholar 9 weeks ago, created an answer that has been accepted. For A: How to update hg19 vcf genomic co-ordinate to LRG/RefSeq cDNA co-ordinate
Popular Question 12 months ago, created a question with more than 1,000 views. For Haplotype Phasing from Sequence Data!
Great Question 14 months ago, created a question with more than 5,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 14 months ago, created a question with more than 1,000 views. For Haplotype Phasing from Sequence Data!
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Phytoviruses are found in human brain: how to evaluate it?
Popular Question 20 months ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 23 months ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 23 months ago, created a question with more than 1,000 views. For VCF to ANNOVAR format
Popular Question 2.4 years ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Scholar 2.4 years ago, created an answer that has been accepted. For A: How to update hg19 vcf genomic co-ordinate to LRG/RefSeq cDNA co-ordinate
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Phytoviruses are found in human brain: how to evaluate it?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 3.6 years ago, created a question with more than 1,000 views. For VCF to ANNOVAR format
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Contamination Check using HET/HOM
Supporter 3.7 years ago, voted at least 25 times.
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Phytoviruses are found in human brain: how to evaluate it?
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Phytoviruses are found in human brain: how to evaluate it?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1209 users visited in the last hour