User: Titus

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Titus600
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1 year, 3 months ago
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Posts by Titus

<prev • 191 results • page 1 of 20 • next >
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Comment: C: Varscan2 mutational calling analysis
... I think there is a miss understood between SNP and SNV variant. But if i'm wrong about miss understood, SNPs is defined from population frequency. So to get this kind of information you need databases like dbSNP gnomAD ExAC etc ...
written 5 weeks ago by Titus600
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Comment: C: Basics about sequencing/alignment and variant calling
... > It can occurs that the human dna contain more than 2 alleles because > some cells contain a mutation/variation and others not? In an haploid > case, can we expect alleles? Yes but most of case it is mosaic cells (sub-population of cells) which have low coverage. > When we obtain th ...
written 11 weeks ago by Titus600
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Comment: C: Alignment & Variant Calling explanation SNP and SNV.
... In which organism you work ? http://csb5.github.io/lofreq/commands/#call if you look this page it seems they use dbsnp to call SNP for human by default : > If you are dealing with human samples (or large genomes in general) we > recommend the use of -s (source quality) in combination with - ...
written 12 weeks ago by Titus600
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Comment: C: Need help to understand mutalyzer variant desciption
... Ok my bad you right. Thank you ...
written 12 weeks ago by Titus600
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Comment: C: Mutation position in COSMIC
... It seems you discovered a bug :) I checked on hg19 and it's looks like a G on this position but your gene doesn't exist on hg19 ... what a mess .. ...
written 3 months ago by Titus600
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Comment: C: Need help to understand mutalyzer variant desciption
... ok so that make sens, and at the end this link : https://mutalyzer.nl/name-checker?description=NM_001258271.1%3Ac.1484delC work because CDS for position 1484 are the same between the 2 NM. Thank you for the answer it help :) Do you have an idea for the second part of the question ? Best ...
written 3 months ago by Titus600
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Comment: C: Need help to understand mutalyzer variant desciption
... Thank you Emily, I got an error with https://mutalyzer.nl/name-checker?description=NM_001258271.1%3Ac.1682delC so i looked to https://mutalyzer.nl/name-checker?description=NM_001258271.1%3Ac.1682del and it works but if i look the genomic region it's not the same (no presence of the poly C). I saw ...
written 3 months ago by Titus600
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Need help to understand mutalyzer variant desciption
... He there , I was checking my cDNA annotation (annotates by VEP ) on web and i agreed in lot of point with mutalyser until this example concerning this variant NM_000249.3:c.1484delC ( https://mutalyzer.nl/name-checker?description=NM_000249.3%3Ac.1484delC ) (with genomic position on hg19 : chr3-37 ...
snp written 3 months ago by Titus600 • updated 3 months ago by jfjlaros10
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Comment: C: BWA error [bns_restore_core] Parse error reading ref.fa.amb- After and despite r
... ***Should I concatenate only chr1-22, X, Y, M?*** What did concatenated plus that ? Sure you have to concatenated only that ! How did syou concatenated it by the way ? I get my hg19 on ucsc like downloading ref chromosome by chromosome and concatenated them ...
written 3 months ago by Titus600
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Comment: C: gene expression data for subtype cancer
... may be that : https://www.ncbi.nlm.nih.gov/sra/?term=nasopharyngeal+RNA-seq https://www.ncbi.nlm.nih.gov/sra/?term=stomach+RNA-seq ...
written 3 months ago by Titus600

Latest awards to Titus

Commentator 6 months ago, created a comment with at least 3 up-votes. For C: BWA: Why paired reads mapped to different chromosome?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: BWA: Why paired reads mapped to different chromosome?
Centurion 8 months ago, created 100 posts.
Supporter 10 months ago, voted at least 25 times.
Appreciated 12 months ago, created a post with more than 5 votes. For C: BWA: Why paired reads mapped to different chromosome?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: BWA: Why paired reads mapped to different chromosome?
Rising Star 12 months ago, created 50 posts within first three months of joining.
Scholar 13 months ago, created an answer that has been accepted. For C: finding homologs in human
Teacher 13 months ago, created an answer with at least 3 up-votes. For C: where to find a list of often mutated or lost regions in cancers
Scholar 14 months ago, created an answer that has been accepted. For C: finding homologs in human

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