User: yh362

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yh36230
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Posts by yh362

<prev • 10 results • page 1 of 1 • next >
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vcf file has an empty sample id
... It seems like my VCF's header contains at least an empty smaple ID. I am not sure how to figure out where it goes wrong because, if I run awk 'print NF', all lines have the same number of fields. When I ran bcftools, it told me "[E::bcf_hdr_add_sample] Empty sample name: trailing spaces/tabs in th ...
vcf bcftools snp written 8 months ago by yh36230 • updated 8 months ago by lakhujanivijay5.3k
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transmitted and untransmitted alleles
... Sorry the question seems very basic, yet I coulnd't find it on google. When browsing through the HapMap3 project release, I see - Files are organised in a snps x haplotypes format, so every row represents a SNP and every column a haplotype. - The first row (header row) contains t ...
hapmap haplotype snp phasing written 11 months ago by yh36230 • updated 11 months ago by Kevin Blighe66k
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non conversion rate in BS-sq
... Sorry if this question seems dumb. I have read some papers and all of them say that non-conversion rate was calculated from the chloroplast genome. But exactly how this calculation is done? And after the non-conversion rate is calculated, how does this affect downstream analysis? For example, bismar ...
methylation bismark bs-sq written 14 months ago by yh36230
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Design for gene network analysis with WGCNA
... I have lots of RNA-seq data from various tissues and conditions, etc of a polyploid plant, and wanna take a look at how the two subgenomes behave in terms of co-expression network. Can I pool all these RNA-seq data together? Or is it more reasonable to split them by tissues and conditions and constr ...
wgcna network co-expression written 14 months ago by yh36230 • updated 14 months ago by andres.firrincieli950
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Difference between samtools cat and the unix command cat?
... I am wondering, if I want to concatenate several .bam files, what's the difference between using samtools cat and the unix command cat? ...
samtools unix written 15 months ago by yh36230 • updated 15 months ago by benformatics2.0k
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Newbie questions about Bismark deduplication step and --bedgraph output
... On Bismark user manual, it says the following: > The script deduplicate_bismark is supposed to remove alignments to the same position in the genome from the Bismark mapping output (both single and paired-end SAM/BAM files), which can arise by e.g. excessive PCR amplification. Sequences which ali ...
bisulfite seq epigenetics bismark dna methylation written 15 months ago by yh36230
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Bias in GO enrichment analysis for non-model organsim?
... I am currently working on a non-model plant species and after running interproscan, I realized that only a little over half (~38000 out of 63000 genes) get at least one GO term assigned to it. That way, if I were to do a GO enrichment analysis, some gene of interest (say, differentially expressed ge ...
interproscan gene ontology topgo go enrichment written 15 months ago by yh36230 • updated 15 months ago by Philipp Bayer6.8k
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Visualizing gene density along the chromosome
... I want to visualize gene density along several chromosomes as a heatmap like the supplementary figure 13 in this link https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-019-0405-z/MediaObjects/41588_2019_405_MOESM1_ESM.pdf Hope someone could recommend some python or R packages for doing ...
python R written 16 months ago by yh36230 • updated 16 months ago by igor11k
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Comment: C: Biopython chromosome drawing with coloring
... Thanks! I didn't know karyoplotteR before, but it seems promising! ...
written 16 months ago by yh36230
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Biopython chromosome drawing with coloring
... Hi, I am using Bio.graphics.BasicChromosome module. I want to draw a allotetraploid plant genome so that chromosomes coming from different ancestral species have different color coding. I know how to draw the backbone chromosomes but I don't quite get how to fill in colors. Also, for some chromosome ...
biopython written 16 months ago by yh36230

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