User: reza
reza • 190
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i am here to learn
Posts by reza
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... thanks, your suggested way worked fine. ...
written 9 days 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 9 days ago by
reza • 190
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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 10 days ago by
reza • 190
• updated
10 days ago by
Pierre Lindenbaum ♦ 111k
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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 23 days ago by
reza • 190
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... i annotated vcf file using snpeff but i do not now how find LOFs ...
written 5 weeks ago by
reza • 190
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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 5 weeks 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 4 months ago by
reza • 190
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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 4 months ago by
reza • 190
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Comment:
C: CNV detection using BAM file
... Thanks vchris_ngs, I will use your advice. ...
written 4 months ago by
reza • 190
0
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Comment:
C: CNV detection using BAM file
... Thanks for your clear response Eric. ...
written 4 months ago by
reza • 190
Latest awards to reza
Popular Question
3 months ago,
created a question with more than 1,000 views.
For building database in snpEff
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For how to select longest isoform per gene in gtf
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4 months ago,
created a question with more than 1,000 views.
For building database in snpEff
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For building database in snpEff
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19 months ago,
created a comment with at least 3 up-votes.
For C: Problems with Trimmomatic PE output files
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