User: reza.jabal

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reza.jabal350
Reputation:
350
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Location:
New York, USA
Twitter:
mjabal
Last seen:
1 week, 1 day ago
Joined:
4 years, 12 months ago
Email:
r*********@yahoo.co.uk

Posts by reza.jabal

<prev • 91 results • page 1 of 10 • next >
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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 4 weeks ago by reza.jabal350
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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 3 months ago by reza.jabal350
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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 3 months ago by reza.jabal350
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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 3 months ago by reza.jabal350
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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 3 months ago by reza.jabal350
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Answer: A: Stats on WGS variant calls
... Welcome to the world of bash scripting! Lets have your Funcotator results in Funcotator.txt: For missense count: `grep -w 'MISSENSE' Funcotator.txt | wc -l` For nonsense count: `grep -w 'NONSENSE' Funcotator.txt | wc -l` For intronic count: `grep -w 'INTRON' Funcotator.txt | wc -l` For exonic co ...
written 7 months ago by reza.jabal350
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Comment: C: Get gene counts from *.sam file and annotation
... You are on track! 1) Download a bed file containing the coordinates of all Gencode genes (You can download it from the UCSC table browser). 2) Convert your bam to bed: samtools view -bq 20 -F 1796 "XXX.bam" | bamToBed -i stdin > XXX.bed 3) In bedtools run: bedtools intersect -a XXX. ...
written 16 months ago by reza.jabal350
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Comment: C: Get gene counts from *.sam file and annotation
... To get the gene counts you need to annotate your aligned reads first (based on the coordinates in the 3rd and the 4th column!) ...
written 16 months ago by reza.jabal350
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Answer: A: pfam enrichment analysis of RNAseq data
... Have you tried [Enrichr][1]? Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 20 ...
written 19 months ago by reza.jabal350
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Comment: C: How to update hg19 vcf genomic co-ordinate to LRG/RefSeq cDNA co-ordinate
... You're welcome! Can you please also accept the answer so it will be added to the resolved list. ...
written 22 months ago by reza.jabal350

Latest awards to reza.jabal

Popular Question 4 months ago, created a question with more than 1,000 views. For Haplotype Phasing from Sequence Data!
Great Question 7 months ago, created a question with more than 5,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 7 months ago, created a question with more than 1,000 views. For Haplotype Phasing from Sequence Data!
Teacher 11 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 13 months ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 16 months ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 16 months ago, created a question with more than 1,000 views. For VCF to ANNOVAR format
Popular Question 21 months ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Scholar 22 months 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 24 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 3.0 years ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 3.0 years ago, created a question with more than 1,000 views. For VCF to ANNOVAR format
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Contamination Check using HET/HOM
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Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Phytoviruses are found in human brain: how to evaluate it?
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Phytoviruses are found in human brain: how to evaluate it?

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