User: ThulasiS

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ThulasiS60
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Posts by ThulasiS

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Comment: C: ClustAGE error on Linux - "Support directory 'bin' is not present"
... Hi How can I visualize heat map on iOTL? Did you get the results for your data? I am having trouble in visualization part. ...
written 7 months ago by ThulasiS60
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Comment: C: Is it advisable to include reference genome for pan-genome anlysis when working
... Thank you Ram Sorry for my format ...
written 7 months ago by ThulasiS60
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Comment: C: Is it advisable to include reference genome for pan-genome anlysis when working
... I didn't get you Devon Ryan. But I'll explain here my concerns. I used Roary pipeline to construct pan-genome. I am anlyzing livestock associated strains but I have reference strain from human origin. So I was thinking if we include reference strain for pangenome size calculation, the size maybe v ...
written 7 months ago by ThulasiS60
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Is it advisable to include reference genome for pan-genome anlysis when working on specific type strains?
... I constructed and analyzed pan-genome but now I got this doubt: Is it advisable to include reference genome for pan-genome analysis when working on specific type strains? Please suggest me. Thank you ...
genome pangenome written 7 months ago by ThulasiS60 • updated 7 months ago by RamRS19k
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Comment: C: Flower plot in R ?
... Hi Thank you for your jiffy reply. I too added the same but before the original plotrix::draw.circle line. So, I didn't get result but now we go it. Thank you ...
written 7 months ago by ThulasiS60
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Comment: C: Flower plot in R ?
... Thanks for your answer your function gives exact output. But if I wish to draw an another circle within the circle with same center (i.e. two circle with same center but different radius), what modifications we need to do? I tried draw.circle function with reduced radius but it was giving two differ ...
written 7 months ago by ThulasiS60
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Answer: A: Is it possible to do enrichment analysis for selected genes just with GO number
... I found my answer finally We can do it in blast2go. First map the whole protein database which act as universe and retrieve annotation file from your results in blast2go and then upload your test ids list and run gene enrichment analysis. Thats all. ...
written 11 months ago by ThulasiS60
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Comment: C: Is it possible to do enrichment analysis for selected genes just with GO number
... I am using blast2go to get GO numbers. When I am doing Fisher's exact test it was saying no result. Then I read about topGO and GOstats packages from R. So, I asked here. Now, I understood we need two gene sets for enrichment analysis. One acts as universe. Thank you ...
written 11 months ago by ThulasiS60
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Is it possible to do enrichment analysis for selected genes just with GO number in topGO?
... I would like to get Fisher's exact Test, FDR value for certain selected genes. But later i understood that can be done only if we have expression data along with GO number. But in one article they did without any expression data. I am confused, really is it possible to carry gene enrichment analysis ...
R enrichment analysis written 11 months ago by ThulasiS60
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Answer: A: Regarding Whole Genome Visualization
... I suggest you to use MAUVE for visualization of your contigs and part from that have a look at CCT-view for whole genome visualization. Refer: J.R. Grant, A.S. Arantes, P. Stothard, “Comparing thousands of circular genomes using the CGView Comparison Tool” BMC Genomics 13, 202, 2012. It may help yo ...
written 14 months ago by ThulasiS60

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Scholar 11 months ago, created an answer that has been accepted. For A: Is it possible to do enrichment analysis for selected genes just with GO number

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