User: Marcin Grzybowski

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Posts by Marcin Grzybowski

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How to import vcf with multi sample?
... Thank you very much for advice. SnpMatix seems to be very useful. Marcin ...
written 3.4 years ago by Marcin Grzybowski0
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Comment: C: How to import vcf with multi sample?
... Thank you for your reply and advice. Yes, it is what i would like to do. I thought that maybe easy way to make downstream analysis. So as i understand i can have to use readGT() to get proper information about genotype?  Marcin ...
written 3.4 years ago by Marcin Grzybowski0
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How to import vcf with multi sample?
... Hello, i have large VCF file, which contains 916 samples. Because i am interested in specific region of genom, i create smaller VCF with which looks like this: class: CollapsedVCF dim: 167 916 rowRanges(vcf): GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER info(vcf): Dat ...
vcf readvcf readvcfasvranges written 3.4 years ago by Marcin Grzybowski0
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Comment: C: ggbio circular plot
... Thank you for advice. I run: runsum(coverage(GRanges List), k=50000) and i got Simple Rle List. I can make nice bar with it, however when i try: ggplot() + layout_circle(GRanges object, geom="ideo", radius=30, trackWidth=2, fill=SimpleRleList) it doesn't change my colors. What should i do to cha ...
written 3.4 years ago by Marcin Grzybowski0
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ggbio circular plot
... I have GRanges object with SNP. I would like to mark it on chromosome using circular plot from ggbio by colour scale - so more SNP in particular region deeper color. Is it any simple way to do it? Thank you very much for any advice. Marcin ...
snp ggbio granges written 3.4 years ago by Marcin Grzybowski0 • updated 3.4 years ago by Michael Lawrence11k
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Comment: C: Non overlaps seqence
... Thank you very much! Now i see it wasn't best idea in this case but it may be usefull in the future. ...
written 3.6 years ago by Marcin Grzybowski0
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Non overlaps seqence
... Hi, i have two Large GRanges object and i try to find ranges which are only in one object. So i think i am looking for opposite function to findOverlaps. Is it any easy way to do it? Thx for any advice. Best, Marcin  ...
granges written 3.6 years ago by Marcin Grzybowski0 • updated 3.6 years ago by Michael Lawrence11k
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Comment: C: Error while forge Bsgenome
... Thx a lot! Marcin ...
written 3.6 years ago by Marcin Grzybowski0
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Error while forge Bsgenome
... Hi, i'm trying to forge Bs genome data package with maize genome Following the vignette I downloaded FASTA file (each for one chromosome) and put it into one folder: marcin@marcin:/media/marcin/ngs/maizeGenome/seed$ ls chr10.fa chr2.fa chr4.fa chr6.fa chr8.fa maize chr1.fa chr3.fa chr5.f ...
bsgnome forge written 3.6 years ago by Marcin Grzybowski0 • updated 3.6 years ago by Hervé Pagès ♦♦ 13k

Latest awards to Marcin Grzybowski

Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to import vcf with multi sample?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For ggbio circular plot

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