User: reza

gravatar for reza
reza190
Reputation:
190
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Trusted
Location:
Iran
Last seen:
1 day, 23 hours ago
Joined:
2 years 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 9 days 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 9 days 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 10 days ago by reza190 • updated 10 days ago by Pierre Lindenbaum111k
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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 23 days 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 5 weeks 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 5 weeks 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 4 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 4 months ago by reza190
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Comment: C: CNV detection using BAM file
... Thanks vchris_ngs, I will use your advice. ...
written 4 months ago by reza190
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Comment: C: CNV detection using BAM file
... Thanks for your clear response Eric. ...
written 4 months ago by reza190

Latest awards to reza

Popular Question 3 months ago, created a question with more than 1,000 views. For building database in snpEff
Popular Question 3 months ago, created a question with more than 1,000 views. For how to select longest isoform per gene in gtf
Popular Question 4 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 building database in snpEff
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Problems with Trimmomatic PE output files

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