User: vlad1

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vlad10
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Posts by vlad1

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3 millions de novo RNA mammalian contigs. Too many?
... I wonder if somebody saw similar number of contigs? Do you consider them as real splicing variants or assembling errors? The Trinity assembly was made from HiSeq 2x150 paired-end reads, ~110 mammalian brain samples. Totally ~ 6.3 total billions read pairs, 1,907,297 Mbases. I can't say how many ...
assembly next-gen rna-seq written 9 months ago by vlad10 • updated 9 months ago by genomax59k
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Answer: A: Variant Effect Predictor For Two Individuals Output
... You can try to use GEMINI to search VEP output with various disease association models (recessive,dominant, compound etc.).  ...
written 3.8 years ago by vlad10
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Comment: C: memory usage and run time for VEP whole genome variant annotation?
... Thanks! it worked. greatly reduced memory footprint and took about 10 hours to process 42M variants on 8 cpus. I used --fork 6: --force_overwrite -i G85829.vcf --cache --assembly GRCh37 --offline --individual all --fork 6 --sift b --polyphen b --symbol --numbers --biotype --total_length -o output - ...
written 3.8 years ago by vlad10
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memory usage and run time for VEP whole genome variant annotation?
... Hi,   What memory usage and run time for VEP whole genome variant annotation? I tried annotate a 5 sample Illumina 30x coverage whole genome VCF:  perl /ensembl-tools-release-78/scripts/variant_effect_predictor/variant_effect_predictor.pl --force_overwrite -i G85829.vcf --cache --assembly GRCh37 ...
genome ensembl vep snp written 3.8 years ago by vlad10 • updated 3.8 years ago by EnsemblWill560
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Sg-Adviser Exception In Thread "Pool-2-Thread-1" Java.Lang.Arrayindexoutofboundsexception
... it returns error when I try to open native genome annotation file with suggested coding and splising variant filter C:\Users\vmorozov>java -showversion java version "1.7.0_06" Java(TM) SE Runtime Environment (build 1.7.0_06-b24) Java HotSpot(TM) 64-Bit Server VM (build 23.2-b09, mixed mode) C:\ ...
written 5.2 years ago by vlad10 • updated 5.1 years ago by Biostar ♦♦ 20

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Popular Question 3.7 years ago, created a question with more than 1,000 views. For memory usage and run time for VEP whole genome variant annotation?

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