User: reza
reza • 190
- Reputation:
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i am here to learn
Posts by reza
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... thanks, your suggested way worked fine. ...
written 3 months ago by
reza • 190
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... 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
reza • 190
6
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... 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 ...
written 3 months ago by
reza • 190
• updated
3 months ago by
Pierre Lindenbaum ♦ 114k
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... 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
reza • 190
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... i annotated vcf file using snpeff but i do not now how find LOFs ...
written 4 months ago by
reza • 190
2
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... 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 ...
written 4 months ago by
reza • 190
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... 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
reza • 190
0
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1
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... 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
reza • 190
0
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Comment:
C: CNV detection using BAM file
... Thanks vchris_ngs, I will use your advice. ...
written 8 months ago by
reza • 190
0
votes
1
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662
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1
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Comment:
C: CNV detection using BAM file
... Thanks for your clear response Eric. ...
written 8 months ago by
reza • 190
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For C: Problems with Trimmomatic PE output files
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