User: Martina

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Martina10
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22 hours ago
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3 months, 4 weeks ago
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Posts by Martina

<prev • 11 results • page 1 of 2 • next >
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Bam QC, GC content
... Hello, I would like to ask you for advice with the assessment of BAM quality, especially QC content. This is the result of quality check by qualimap, exome sequencing with NEB and TWIST, only on-target regions are assessed. Have you got some idea why GC content is so shifted? It is a cancer sample, ...
next-gen written 12 days ago by Martina10
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function install.extras in R is not found
... Hello, I wanted to install and use NMF in R but I get an error: > Error in install.extras("NMF") : could not find function > "install.extras" Could you please advice me how to install install.extras to R? Thank you very much, Martina ...
R written 7 weeks ago by Martina10 • updated 16 days ago by Biostar ♦♦ 20
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Comment: C: Amount of variants increased after bedtools subtract
... Hello Fin, thank you very much for your answer. Now I see that by default, bedtools filters out only variants with 100% overlap with bed file, so if I have a long variant covering 2 regions in bed file and I don't have -A option (which filters out variants with at least 1bp overlap), bedtools "touch ...
written 7 weeks ago by Martina10
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Comment: C: Amount of variants increased after bedtools subtract
... Ok, thank you, next time I will focuse on it ...
written 7 weeks ago by Martina10
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Amount of variants increased after bedtools subtract
... Hello all, I have vcfs from exome sequencing and I wanted to filter out from it variants from homopolymer regions with bed file covering the homopolymer regions by bedtools subtract, but to my surprise, amount of variants (rows in the file) increased after bedtools subtract. The command I used was ...
next-gen written 7 weeks ago by Martina10 • updated 7 weeks ago by finswimmer12k
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Comment: C: How to choose variants for viewing in IGV?
... Dear Daiana, that's exactly that kind of answer I needed, thank you very much!! I also found this great tutorial about what sequencing artefacts look like in IGV, https://bioinformatics-core-shared-training.github.io/intro-to-IGV/InspectingVariantsInIGV.html and this interesting paper https://www.nc ...
written 3 months ago by Martina10
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Answer: A: How to calculate base substitution mutation frequency (C>T T>A C>G T
... Hello, isn't maftools plotmafSummary what you are looking for? https://www.bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html ...
written 3 months ago by Martina10
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Comment: C: How to choose variants for viewing in IGV?
... Sure, I am processing exome tumor-normal paired data and I am searching for somatic variants. We are not focusing on structural variants because the DNA is amplified. I have bam files created by BWA-mem and vcf files from freebayes filtered out with several filters. Now I would like to make an overv ...
written 3 months ago by Martina10
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How to choose variants for viewing in IGV?
... Hello guys, do you have some "verified" strategy about how to choose of variants for viewing in IGV? :) Thank you very much, Martina ...
next-gen written 3 months ago by Martina10 • updated 3 months ago by dganiewich90
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Comment: A: VCF INFO interpretation
... Thank you very much! I still have several variables about which I am not 100% that I fully understand its meaning. I wanted to post here everything, but I don't have time to do it now, so at this moment I really appreciate your answers and I will post progress here later. Bye for now :) Martina ...
written 3 months ago by Martina10

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