User: reza.jabal

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reza.jabal330
Reputation:
330
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Trusted
Location:
New York, USA
Twitter:
mjabal
Last seen:
2 days, 12 hours ago
Joined:
4 years, 5 months ago
Email:
r*********@yahoo.co.uk

Posts by reza.jabal

<prev • 86 results • page 1 of 9 • next >
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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 5 weeks ago by reza.jabal330
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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 10 months ago by reza.jabal330
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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 10 months ago by reza.jabal330
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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 12 months ago by reza.jabal330
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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 16 months ago by reza.jabal330
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Answer: A: How to update hg19 vcf genomic co-ordinate to LRG/RefSeq cDNA co-ordinate
... Through two steps you can achieve this: (1) Convert your cDNA nucleotide change to genomic coordinates using [TransVar][1] and generate a VCF file according to the hg19 assembly. (2) Use [GATK VCF union module][2] or vcftools to identify common variants between the two files! Hope it helps! ...
written 16 months ago by reza.jabal330
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Comment: C: Remap variants from hg19 to LRG/RefSeq
... Can you provide an instance of your second vcf? ...
written 16 months ago by reza.jabal330
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Comment: C: How to extract PRDM9 binding motifs in bed format?
... Alex thanks a lot for your suggestion. It is super helpful! ...
written 16 months ago by reza.jabal330
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Comment: C: How to extract PRDM9 binding motifs in bed format?
... Thanks a lot for your suggestion. Seems like a handy package that helps solving the problem! ...
written 16 months ago by reza.jabal330
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Comment: C: How to extract PRDM9 binding motifs in bed format?
... Thank you for your suggestion, I am looking for a database that such motifs could be pulled from in bed format? ...
written 17 months ago by reza.jabal330

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Great Question 26 days ago, created a question with more than 5,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 26 days ago, created a question with more than 1,000 views. For Haplotype Phasing from Sequence Data!
Teacher 5 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 7 months ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 10 months ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 10 months ago, created a question with more than 1,000 views. For VCF to ANNOVAR format
Popular Question 15 months ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Scholar 16 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 17 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 2.5 years ago, created a question with more than 1,000 views. For BWA indexer fails to generate fasta.sa file!
Popular Question 2.5 years ago, created a question with more than 1,000 views. For VCF to ANNOVAR format
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Contamination Check using HET/HOM
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Teacher 3.2 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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