User: reza

gravatar for reza
reza190
Reputation:
190
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Trusted
Location:
Iran
Last seen:
1 month ago
Joined:
2 years, 3 months ago
Email:
r********@gmail.com

i am here to learn

Posts by reza

<prev • 94 results • page 1 of 10 • next >
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Comment: C: how to extract gene name for LOF (loss of function) variants
... thanks, your suggested way worked fine. ...
written 3 months ago by reza190
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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 3 months ago by reza190
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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 3 months ago by reza190 • updated 3 months ago by Pierre Lindenbaum114k
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Comment: C: how to extract LOF variants from vcf file?
... i found that i must add -lof option to my command to vcf annotation as following: java -jar snpEff.jar eff -v -lof BB_12 WC247_final_snps.vcf > WC247_final_snps_lof.vcf but there is no LOF tags in INFO fields. what part of my work is fault? it is worth to mention that building of database for ...
written 3 months ago by reza190
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Comment: C: how to extract LOF variants from vcf file?
... i annotated vcf file using snpeff but i do not now how find LOFs ...
written 4 months ago by reza190
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how to extract LOF variants from vcf file?
... hi all i have a vcf file resulted from whole genome sequencing project and now i want to extract heterozygote and homozygote loss function (LOF) non synonymous SNPs. how can i do it? thanks in advance ...
vcf loss function variants variants written 4 months ago by reza190
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Comment: C: Correct Trimmomatic adapter sequence file to use?
... if it is possible for you, use [cutadapt][1] and define your own adapters for it to remove them. Although you can create a fasta file includes your adapters for [Trimmomatic][2] [1]: http://cutadapt.readthedocs.io/en/stable/ [2]: http://www.usadellab.org/cms/?page=trimmomatic ...
written 7 months ago by reza190
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Comment: C: how to retrieve sequences from genome
... you can use [extractseq][1] in [EMBOSS][2] [1]: http://emboss.bioinformatics.nl/cgi-bin/emboss/extractseq [2]: http://emboss.sourceforge.net/ ...
written 7 months ago by reza190
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Comment: C: CNV detection using BAM file
... Thanks vchris_ngs, I will use your advice. ...
written 8 months ago by reza190
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Comment: C: CNV detection using BAM file
... Thanks for your clear response Eric. ...
written 8 months ago by reza190

Latest awards to reza

Popular Question 10 weeks ago, created a question with more than 1,000 views. For variant calling after mapping via bwa mem
Popular Question 6 months ago, created a question with more than 1,000 views. For building database in snpEff
Popular Question 6 months ago, created a question with more than 1,000 views. For how to select longest isoform per gene in gtf
Popular Question 8 months ago, created a question with more than 1,000 views. For building database in snpEff
Popular Question 9 months ago, created a question with more than 1,000 views. For building database in snpEff
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: Problems with Trimmomatic PE output files

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