User: reza

gravatar for reza
reza210
Reputation:
210
Status:
Trusted
Location:
Iran
Last seen:
2 weeks, 3 days ago
Joined:
2 years, 8 months ago
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r********@gmail.com

i am here to learn

Posts by reza

<prev • 101 results • page 1 of 11 • next >
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Comment: C: variant calling in mitochondria using whole genome sequencing
... when i set -ploidy 100, numbers of identified SNPs increased from 23 to 593 ! without apply of -ploidy on 100, my results (23 SNPs) are correct? ...
written 3 months ago by reza210
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variant calling in mitochondria using whole genome sequencing
... i performed variant calling in mitochondria using whole genome sequencing data by GATK UnifiedGenotyper. Genotype of some SNPs specially those are in D-loop region is heterozygote (0/1). Is it due to heteroplasmy? ...
mitochondria snp written 3 months ago by reza210
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Comment: C: several effect for one SNP annotated by SNPeff
... i did it, i described it in my question ...
written 3 months ago by reza210
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Comment: C: several effect for one SNP annotated by SNPeff
... i have vcf file resulted from standard workflow of variant calling (fastq files mapped to reference genome, post-alignment steps, variant calling by samtools). under study species is Bactrian camel ...
written 3 months ago by reza210
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Comment: C: How can I call somatic CNV in tumor samples with no reference (control) samples?
... do you searched about Control-free? ...
written 3 months ago by reza210
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Comment: C: several effect for one SNP annotated by SNPeff
... thanks Kevin ANNOVAR can help me i guess. i have reference (fasta) file and gff3 file of under study organism. i read ANNOVAR manual for annotation of vcf file by gff3 file but it puzzled me because all the examples are about a human that has all kind of required data. can you help me to do that? a ...
written 3 months ago by reza210
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several effect for one SNP annotated by SNPeff
... hi i annotated one vcf file using SNPeff and now some SNPs have several effect instead one effect, for example: ANN=A|splice_acceptor_variant&splice_donor_variant&intron_variant|HIGH|LOC105079267|gene19881|transcript|rna26374|protein_coding|4/6|c.2134+1C effect of splice_acceptor_vari ...
annotation snpeff snp written 3 months ago by reza210
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Comment: C: how to extract gene name for LOF (loss of function) variants
... thanks, your suggested way worked fine. ...
written 7 months ago by reza210
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Comment: C: how to extract gene name for LOF (loss of function) variants
... thanks Pierre, your program worked but i want variants that have LOF tag (in my file 466 variants from 994779 variants). your program give me a file with 1526324 row! ...
written 7 months ago by reza210
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how to extract gene name for LOF (loss of function) variants
... hi everyone i annotated my VCF file using snpEff, now i want gene names for LOF (loss of function) variants. how can i do it? anyone can help me? for example in following variant, name of TRAPPC8 gene must be extracted. KN271071.1 10335196 . G A 217.0 PASS DP=35;VDB=0.8177;SGB=-0.693136;MQSB=0 ...
snpeff lof variants written 7 months ago by reza210 • updated 7 months ago by Pierre Lindenbaum118k

Latest awards to reza

Popular Question 7 weeks ago, created a question with more than 1,000 views. For cygwin error when i try to install platypus (variant caller)
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Augustus running error
Centurion 3 months ago, created 100 posts.
Popular Question 5 months ago, created a question with more than 1,000 views. For variant calling after mapping via bwa mem
Popular Question 5 months ago, created a question with more than 1,000 views. For cygwin error when i try to install platypus (variant caller)
Popular Question 5 months ago, created a question with more than 1,000 views. For how to select longest isoform per gene in gtf
Popular Question 6 months ago, created a question with more than 1,000 views. For variant calling after mapping via bwa mem
Popular Question 10 months ago, created a question with more than 1,000 views. For building database in snpEff
Popular Question 10 months ago, created a question with more than 1,000 views. For how to select longest isoform per gene in gtf
Popular Question 12 months ago, created a question with more than 1,000 views. For building database in snpEff
Popular Question 13 months ago, created a question with more than 1,000 views. For building database in snpEff
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Problems with Trimmomatic PE output files

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