User: jan

gravatar for jan
jan140
Reputation:
140
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Location:
Sydney, Australia
Last seen:
2 months, 1 week ago
Joined:
5 years, 11 months ago
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j**********@gmail.com

Posts by jan

<prev • 40 results • page 1 of 4 • next >
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Comment: C: VEP is returning MOTIF_NAME values not recognised by Ensembl
... Hi, Im having the same issue. Have you found a solution to search for those motif based on VEP motif (ENSM..........). ? ...
written 10 weeks ago by jan140
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Comment: C: filter_vep not filtering according to my --filter criteria
... Thanks for the correction Ben. It is now working as intended. ...
written 3 months ago by jan140
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Comment: C: filter_vep not filtering according to my --filter criteria
... Thanks Ben. I dont think --gz flag was the issued. I still can get the ouput without the --gz flag. But variants in my outputs dont passed all of the filters When I combined all my filters in one line such as below without the --gz flag, i get my desired output. ie variants passing all my filters. ...
written 3 months ago by jan140
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filter_vep not filtering according to my --filter criteria
... Hi, I'm trying to filter my VCFs using filter_vep ([https://asia.ensembl.org/info/docs/tools/vep/script/vep_filter.html][1]) following certain criteria. Variants in my output need to pass all filters. filter_vep \ --input_file input.vcf.gz \ --output_file out.vcf \ ...
filter_vep vep written 3 months ago by jan140 • updated 3 months ago by Ben_Ensembl1.6k
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Hide small indels from PacBio long read sequencing on IGV
... Hi, I'm trying to view structural variants (>50bp) from PacBio long read sequencing on IGV. I have been unable to hide the small indels (likely errors) using these settings: ∗ Alignment Track Options: Hide indels < 10 bases ∗ Coverage Track Options: Coverage allele-fraction threshold: 0.25 ∗ ...
pacbio igv written 15 months ago by jan140
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Comment: C: Automatic IGV snapshot script
... Hi Steve, I'm trying to use your tool to view bam files located on a remote server. I'm getting an error when I tried running the demo. See below. Could you please advice how to fix or troubleshoot this error. Thank you. Read 4 regions xdpyinfo: unable to open display ":1". Open Xvfb port found ...
written 15 months ago by jan140
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Comment: C: Annotation for SV and CNV
... Is this tool suitable for SVs sequenced from PacBio long reads and called using Sniffle? ...
written 16 months ago by jan140
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Prioritizing structural variants and CNV
... Hi All, I'm pretty new in analysing SV and CNV. We have WGS PacBio long reads germline sequencing reads that have been aligned using pbalign tool to reference sequences (GRCh37/hg19). Variants were called using the variantCaller.py from GenomicConsensus package (https://github.com/PacificBioscienc ...
sv pacbio cnv written 16 months ago by jan140 • updated 16 months ago by WouterDeCoster45k
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(Closed) Export impact factor and numbers cited by to Endnote
... Hi, I want to include number of papers cited a certain journal (can be obtained from google scholar) and the journal current impact factor to my references. Is there a tool to export such information from google scholar to endnote? or Excel, or any relevant working sheet. I have 300+ citations t ...
endnote written 2.3 years ago by jan140
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Comment: C: tools to calculate Exac population specific frequency
... I ended up following above suggestion. MAF (mutation allele format) is a format of my variant file. My sequencing vcf files were initially anonated with snpEff and in-house qSNP. So what we did was to re-annotate vcf files using VEP and use their ExAC plugin which can calculate frequency from AN, ...
written 2.7 years ago by jan140

Latest awards to jan

Great Question 4 months ago, created a question with more than 5,000 views. For TCGA MSI status
Popular Question 13 months ago, created a question with more than 1,000 views. For filter multiple VCF files using snpSift
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Mutalyzer: Multiple hgvs names
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Mutalyzer: Multiple hgvs names
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Mutalyzer: Multiple hgvs names
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Mutalyzer: Multiple hgvs names
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Extract each annotation in 'info' column in snpEff output
Popular Question 3.2 years ago, created a question with more than 1,000 views. For filter multiple VCF files using snpSift
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Predicting functional effects of a mutation
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Extract each annotation in 'info' column in snpEff output
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Predicting functional effects of a mutation
Popular Question 3.8 years ago, created a question with more than 1,000 views. For problem to download 1000genome database using ANNOVAR
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Question : Annotating dbNSFP using snpSIFT , problem with index
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Predicting functional effects of a mutation

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