User: Max Ivon

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Max Ivon110
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Posts by Max Ivon

<prev • 38 results • page 1 of 4 • next >
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Comment: C: how to get exact break point in COSMIC fusion gene?
... The problem is that COSMIC arrange data from different sources and exact breakpoints are not always known just becaase the source experiment employed rna-seq - genome break point just can be grasped in this case. If you want to determine the spectrum of breakpoints of ALK fusions I would recommend y ...
written 11 days ago by Max Ivon110
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Comment: C: Multiple biopsy issue in MutSig and GISTIC tools
... There are several issues with merging data from different biopsies. When we talk about biopsies taken at the same time point the major is tumor inter- and intra- heterogeneity. When we talk about different time point it is tumor evolution - for example, molecular landscape of metastatic castrate-res ...
written 11 days ago by Max Ivon110
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Answer: A: Database for Somatic Copy Numbers
... If you want to focus on high confidence mutations you may want to have a look at results of the systemic studies like TCGA or ICGC rather than just mutation database. Try cbioportal.org to overview such projects for different tumor types and focus on the one you are interested in. If you dont need t ...
written 12 days ago by Max Ivon110
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Removing fused transcripts from RNA seq data
... Hello! I have performed alignment of paired-end data with tophat with the following options: tophat --no-coverage-search --max-multihits 1 -p 4 -o <...> <...> <...> -G <...> What would be the easiest way to remove read pairs coming from fused transcripts based on annot ...
rna-seq written 5 months ago by Max Ivon110
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Comment: C: Bowtie2-Samtools. Too many degenerate bases
... There is a bug with several version of samtools (dont know which exactly). It results in improper mpileup (reference is not recognised properly and all or major part is substituted with N). Dont know why it helps, so im not sure wether it will help you or no - may be you faced another error, but it ...
written 19 months ago by Max Ivon110
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Comment: C: How does OMIM select the clinically associated variants (SNPs)?
... Yes, OMIM is manually curated (http://www.omim.org/help/faq). Another sources of pathogenic mutations are CLINVAR and HGMD, which are basically also manually curated, but generally contain more mutations (and more false positive ones, keep this in mind). So OMIM does not hide any variants and show e ...
written 19 months ago by Max Ivon110
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Comment: C: samtools mpileup Aborted (Core dumped)
... Are you sure that you have enough Memory for running samtools with this reference? This may be caused simply by the lack of PC resources. Have you previously successfully performed mpileup with this reference on your PC/server? ...
written 19 months ago by Max Ivon110
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Comment: C: Bowtie2-Samtools. Too many degenerate bases
... Try to create a new folder for your reference (ref.fa in samtools command) put it there alone, index it there and perform your commands again with new reference file - so the only thing changed is the destination of reference file. This might help   ...
written 19 months ago by Max Ivon110
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Comment: C: How are the variants called by samtools?
... Did you mean this? samtools mpileup -d $coverage_max -L $coverage_max -E -uf reference.fasta input.bam -P ILLUMINA -Q 30 | bcftools view -bvgc - > calls.bcf bcftools view calls.bcf | vcfutils varFilter -d 30 -a 10 -1 0.001 -2 0.001 -3 0 -4 0.0001 - > calls.vcf     ...
written 19 months ago by Max Ivon110
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Comment: C: NGS hybrid reads
... Yes,  you got it right ...
written 19 months ago by Max Ivon110

Latest awards to Max Ivon

Popular Question 5 months ago, created a question with more than 1,000 views. For Human Exome GC content
Popular Question 15 months ago, created a question with more than 1,000 views. For Human Exome GC content
Popular Question 17 months ago, created a question with more than 1,000 views. For Can'T Find Indels With Samtools (Onyly Get Snps)
Student 19 months ago, asked a question with at least 3 up-votes. For NGS hybrid reads
Scholar 2.4 years ago, created an answer that has been accepted. For A: GATK dbSNP for Ensembl

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