User: thomasbersez

gravatar for thomasbersez
thomasbersez50
Reputation:
50
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Trusted
Location:
Genevia Technologies, Finland
Website:
https://github.com/tbe...
Last seen:
1 week, 6 days ago
Joined:
11 months ago
Email:
t***********@gmail.com

R&N engineer at Genevia Technologies, Finland

Posts by thomasbersez

<prev • 13 results • page 1 of 2 • next >
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Comment: C: SnpEff START/STOP codon not found error
... Sadly no, since it was not mandatory for my project to use SnpEff I moved to VEP... Not a solution at all I know! ...
written 21 days ago by thomasbersez50
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Tool: AllMine, a flexible pipeline for allele mining
... Hi Everyone ! I just released the first version of my master thesis project, **AllMine, a flexible pipeline for allele mining**. You can use AllMine to discover de novo Single Nucleotide Polymorphism (SNPs) onto next generation sequencing data of various types (RNAseq, WGS, RRGS ect.). AllMine work ...
wgs pipeline snp rna-seq tool written 7 months ago by thomasbersez50
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Comment: C: SnpEff START/STOP codon not found error
... I use `GCF_001659605.1_Manihot_esculenta_v6_genomic.fna` and `GCF_001659605.1_Manihot_esculenta_v6_genomic.gff` both from NCBI genome database. Yes both are from the same build. Thanks for the answer! ...
written 8 months ago by thomasbersez50
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SnpEff START/STOP codon not found error
... Hi! I'm using SnpEff to annotate SNP from Varscan. Since I'm working on Casava, I have build a database locally using Casava genome and its annotation in GFF format. When inspecting the database snpEff reports: snpEff.jar dump snpEff_db | less ... #----------------------------------- ...
software error snpeff snp written 8 months ago by thomasbersez50 • updated 7 months ago by Biostar ♦♦ 20
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MMR for variant calling ?
... Hi, Does anyone ever used MMR or others ambiguous reads resolution tools on bam files before to do variant calling? Does it improvement results accuracy? Thanks for help ! ...
mmr alignment next-gen snp written 9 months ago by thomasbersez50
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Random SNPs simulation?
... Hi everyone, For an allele mining project I need to generate in silico NGS data. I have chosen to use Grinder to do so. I would like to add randomly generated SNPs to my reference genome, is any software available to do that ? Thanks for help! ...
snp written 10 months ago by thomasbersez50 • updated 6 months ago by meenatibiswalcynixit0
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Answer: A: OMA cannot evaluate boolean
... Just an other point, Now I get this error, 1) Mem: 0.017GB (UINT)s=76983683, lostorage=76234752, cond=0 (UINT)s=76983683, historage=157437752, cond=0 strlen(s)=0, s=, s=76983683 strlen(s2)=0, s2=, s2=76983684 Irrecoverable system error gc-14 running Align Aborted (core dumped) wh ...
written 10 months ago by thomasbersez50
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Answer: A: OMA cannot evaluate boolean
... Edit, I have managed to solve the previous error. It was just an error in the `parameters.drw` file ... Sorry for the bothering ^^ ...
written 10 months ago by thomasbersez50
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Answer: A: OMA cannot evaluate boolean
... Hi, Thanks for your quick answer! I get the following message with `OMA -c -d 3`. only_run_dbconv := true # SetRandSeed: SetRand(399990844): Starting database conversion and checks... Process 9707 on pac-1052-998: job nr 1 of 1 Error, (in ConvertGenomes) cannot evaluate boolean ...
written 10 months ago by thomasbersez50
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OMA cannot evaluate boolean
... Hi! I am trying to run OMA standalone on a two proteome test set. All parameters are left to default. I get the following error : OMA -c Starting database conversion and checks... Process 19349 on pac-1052-998: job nr 1 of 1 Error, (in ConvertGenomes) cannot evaluate boolean Any ...
orthologs oma issue bug written 10 months ago by thomasbersez50

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