User: evelyn
evelyn • 20
- Reputation:
- 20
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- New User
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- Last seen:
- 39 minutes ago
- Joined:
- 2 months, 3 weeks ago
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Posts by evelyn
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... I am using `GATK` for variant calling. It works and give results but the number of SNPs found is significantly very low as compared to `samtools`. Is this fine or there is an error? ...
written 1 day ago by
evelyn • 20
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C: R Studio memory on Mac
... I am trying to use them for `Upset` R plot and these are not compressed. ...
written 6 days ago by
evelyn • 20
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... The working code for `UpSet` R plot for `vcf` files is:
rm(list = ls())
library(UpSetR)
library(vcfR)
set1 <- read.vcfR("Set1.vcf")
set2 <- read.vcfR("Set2.vcf")
set3 <- read.vcfR("Set3.vcf")
set4 <- read.vcfR("Set4.vcf")
set5 <- read.vcfR("Set ...
written 6 days ago by
evelyn • 20
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Comment:
C: R Studio memory on Mac
... My Mac has 16 GB memory. ...
written 6 days ago by
evelyn • 20
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... I am trying to import three really big files (each file size >100GB) to R Studio but it complains of memory. I am using this `version`:
platform x86_64-apple-darwin15.6.0
arch x86_64
os darwin15.6.0
system ...
written 6 days ago by
evelyn • 20
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... I am trying to make UpSetR plot for nine vcf files using [working code][1]. However, the output plot shows only five files out of total nine files.
[1]: https://www.biostars.org/p/379679/#379721 ...
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C: upSet R plot for variant calling
... I tried to use the same codes for six vcf files but it shows the plot for five files only. ...
written 7 days ago by
evelyn • 20
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Comment:
C: upSet R plot for variant calling
... It worked. I got same results as of vcf-compare. Thank you! ...
written 8 days ago by
evelyn • 20
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