User: lokraj2003

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lokraj200370
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1 year, 1 month ago
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Posts by lokraj2003

<prev • 30 results • page 1 of 3 • next >
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Consensus sequence from SAM or BAM file?
... I am trying to perform reference-based assembly. Most of the tutorials teach how to create a bam file and view alignemnts in IGV or Tablet. But, I want a assembled genome sequence in fasta format. How can I do that ? Is there any tool or linux syntax available for this purpose ? ...
assembly written 6 weeks ago by lokraj200370
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Answer: A: how to appropriately export datasets from R studio in an appropriate style?
... Maybe you can export into Excel format (.xlsx) instead of .csv format. You can use `xlsx` package to export the data into excel format. ...
written 7 weeks ago by lokraj200370
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How to get log2 fold change of RNA-Seq data for time series experiment?
... I know if there is one control and one treatment group it is pretty straight forward to interpret log 2 fold change. But, I have time course experiment. I have infected cells with viruses and I harvested cells at different time points: o hr, 6 hour, 12 hr and 24 hour. Here o hr is my non-infected co ...
rna-seq written 7 weeks ago by lokraj200370
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Comment: C: Virus RNA Seq reads mapping with salmon
... Thanks for the suggestion and links. I will probably try with ncRNA too. ...
written 8 weeks ago by lokraj200370
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Comment: C: Virus RNA Seq reads mapping with salmon
... I am using Orf virus. Is there any script to combine virus CDS to host genome or you do it manually ? Also, what do you do after getting reads counts ? I mean what tool do you use to separate viral and host reads ? Thank you ...
written 8 weeks ago by lokraj200370
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Virus RNA Seq reads mapping with salmon
... I did RNA seq of the mammalian cells infected with pox virus. Now, I have read files which contains both host and virus reads. I want to align the reads both to host and viral genome. I was thinking I could concatenate the host and virus genome into one file and run salmon against this concatenated ...
rna-seq written 8 weeks ago by lokraj200370 • updated 8 weeks ago by Adrian Pelin2.3k
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Comment: C: Visualizing body organs in R
... Thanks Garan for the link. ...
written 8 months ago by lokraj200370
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Comment: C: Visualizing body organs in R
... I saw some posts about gganatogram on Twitter. That package is really cool. I wish they could add some more species. ...
written 8 months ago by lokraj200370
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Visualizing body organs in R
... I have seen few packages in R where we can plot on human organ templates. One of them is [cerebroViz][1]. But, this package is limited only to brain. Is there any package which lets us use other organs like liver, heart, stomach. Or is there any way we can modify some packages to get such visualiza ...
R ggplot written 8 months ago by lokraj200370 • updated 8 months ago by jared.andrews072.3k
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Comment: C: Genome Diagram in R
... Thank you @h.mon. I will play with it. I guess I will be able to modify this according to my need. ...
written 8 months ago by lokraj200370

Latest awards to lokraj2003

Popular Question 16 days ago, created a question with more than 1,000 views. For Annotation with Prokka or RAST.
Scholar 5 weeks ago, created an answer that has been accepted. For A: how to appropriately export datasets from R studio in an appropriate style?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: how to appropriately export datasets from R studio in an appropriate style?
Popular Question 4 months ago, created a question with more than 1,000 views. For Annotation with Prokka or RAST.

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