User: yh362

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yh36230
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Posts by yh362

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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 1 day 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 7 days ago by yh36230 • updated 5 days ago by andres.firrincieli40
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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 28 days ago by yh36230 • updated 28 days ago by benformatics1.1k
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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 4 weeks 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 5 weeks ago by yh36230 • updated 5 weeks ago by Philipp Bayer6.4k
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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 8 weeks ago by yh36230 • updated 8 weeks ago by igor8.1k
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Comment: C: Biopython chromosome drawing with coloring
... Thanks! I didn't know karyoplotteR before, but it seems promising! ...
written 9 weeks 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 9 weeks ago by yh36230

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