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User: Bioinformatics_NewComer

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Posts by Bioinformatics_NewComer

<prev • 121 results • page 1 of 13 • next >
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Comment: C: Module merging WGCNA
... I'm working step by step, looking into function parameters and reading explanations provided on the tutorial. After rummaging and lost I've posted my query. I can share code and comments if needed to show my inputs. https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tut ...
written 7 hours ago by Bioinformatics_NewComer • 320
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Module merging WGCNA
... Hello all, I'm interested to perform gene co-expression using WGCNA R module. I clean data for samples and remove genes that don't form any cluster. Post cleaning I perform clustering to identify different modules (40 excluding grey). Each module consist different number of genes, I generate list o ...
wgcna expression microarray written 9 hours ago by Bioinformatics_NewComer • 320
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Comment: C: VCF file lacks alternative allele listing for most rs ids
... Can anyone assist with this? Why does this happen. I've ~6K snps with no alternate allele(s) on CHR22 for one of the callings I did. GrCH37, Homo Sapiens, Illumina hiseq 150 bp. ...
written 20 days ago by Bioinformatics_NewComer • 320
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Comment: C: 16S rRNA classification pipeline
... Which region do you've for 16S? Also, there's no assembly needed for 16S data. Do you've Illumina data? ...
written 5 weeks ago by Bioinformatics_NewComer • 320
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Comment: C: Calculate heterozygosity for each SNPs in the bim file.
... > Error: Failed to open Colli_buffalo_diversity.map You have binary format (bim/bam files) acceptable by plink. Use ***--bfile*** ...
written 5 weeks ago by Bioinformatics_NewComer • 320
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Comment: C: Please help with Eagle
... If you're working with CHR9, it could be good to work with genetic map for CHR9 only. ...
written 8 weeks ago by Bioinformatics_NewComer • 320
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Comment: C: Plot local ancestry on chromosome
... Thank you. I'll look into it. ...
written 10 weeks ago by Bioinformatics_NewComer • 320
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Comment: C: Genotype input in matrix eqtl with dosage dataset
... I thought there was flag button on site. This seems spam. ...
written 12 weeks ago by Bioinformatics_NewComer • 320
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Microarray: aroma.affymetrix version for HuGene and HuExon
... Hi All, I'm using aroma.affymetrix R package to get exon level summaries. HuEx-1_0-st-**v2** CDF file I got exon level estimates from instructions at: http://www.aroma-project.org/chipTypes/HuGene-1_0-st-v1/ I cannot get transcript level information (FIRMA scores) working hence I w ...
expression microarray aroma written 3 months ago by Bioinformatics_NewComer • 320 • updated 3 months ago by Kevin Blighe ♦ 37k
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Plot local ancestry on chromosome
... I've per chromosome, per SNP composition from three ancestries using ELIA for each individual. I'd like to plot these information. Is there any R package that can help? Output as: `0.107 0.995 0.898 ` `0.992 0.001 1.007 ` `0.597 1.402 0.001 ` `1.998 0.001 0.001 ` `0.933 0.011 1. ...
ancestry plot written 4 months ago by Bioinformatics_NewComer • 320 • updated 11 weeks ago by bernatgel • 1.7k

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Scholar 4.3 years ago, created an answer that has been accepted. For A: How to output a new alignment containing only sequences with a particular residu
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