User: marcusanaymik

gravatar for marcusanaymik
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United States
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3 years, 5 months ago
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Posts by marcusanaymik

<prev • 7 results • page 1 of 1 • next >
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Affymetrix A/B allele coding to reference 'forward' allele coding manual conversion
... I have a ped file with genotypes from the Genome-Wide Human SNP Array 6.0 array in their native A/B format. I need to convert these to the standard forward coding used by dbsnp and hg19. Does anyone have experience doing this? ...
array allele coding snp affymetrix genotypes written 13 days ago by marcusanaymik10 • updated 2 days ago by Biostar ♦♦ 20
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Number of reference sequence contigs in sam/bam header does not match the number in my fasta
... I created a de novo assembly fasta (masked) which I then used to align the fastq sequences to. I noticed that when building the bowtie 2 reference index for the assembly there were many sequences that were all N's (662,820 to be exact) which I expected from the masking. After alignment I did a grep ...
fasta bowtie2 contig sam bam written 23 months ago by marcusanaymik10 • updated 23 months ago by Brian Bushnell16k
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vcftool negative relatedness values for family members
... I have ran the vcftools relatedness2 analysis on a few families data and some families produce positive relatedness phi scores and some families produce negative phi scores. In the range of + or - [0.1 - 0.3] for child-parents. Is the + - irrelevant? ...
pedigree kinship qc vcftools written 2.7 years ago by marcusanaymik10 • updated 11 days ago by Biostar ♦♦ 20
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Comment: C: RnBeads Pairwise Differential Methylation Tables
... Sorry, I should have replied directly to this. My reply is below. ...
written 2.9 years ago by marcusanaymik10
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Answer: A: RnBeads Pairwise Differential Methylation Tables
... I miss understood that. By pairwise I mean a pair of samples not pair of groups, so strictly 1 case vs 1 control. In my case an affected child vs an unaffected mother. When I tried to put just two samples in the sample_annotation file it does not run at all, it would not run with three samples eithe ...
written 2.9 years ago by marcusanaymik10
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RnBeads Pairwise Differential Methylation Tables
... I am trying to run the differential methylation portion of RnBeads with pairwise.all set. It seems to recognize the pairwise option but I can't find any trace of pairwise data/tables, the group analysis completed however. > diffmeth=rnb.execute.computeDiffMeth(rnb.set,cmp.cols,region.ty ...
pairwise methylation tool rnbeads written 2.9 years ago by marcusanaymik10
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RCircos Heatmap Colors
... Hi I am new to using RCircos and was wondering if anyone knows how to change the heatmap colors? I see there is a function to view the other built-in color ranges but not to set them. Thanks, Marcus ...
R plot colors rcircos heatmap written 3.5 years ago by marcusanaymik10 • updated 23 months ago by jason830110

Latest awards to marcusanaymik

Popular Question 10 months ago, created a question with more than 1,000 views. For RCircos Heatmap Colors
Popular Question 18 months ago, created a question with more than 1,000 views. For RCircos Heatmap Colors

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