User: lokraj2003
lokraj2003 • 70
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Posts by lokraj2003
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... 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 ? ...
written 6 weeks ago by
lokraj2003 • 70
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... 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
lokraj2003 • 70
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... 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 ...
written 7 weeks ago by
lokraj2003 • 70
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... Thanks for the suggestion and links. I will probably try with ncRNA too. ...
written 8 weeks ago by
lokraj2003 • 70
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... 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
lokraj2003 • 70
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... 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 ...
written 8 weeks ago by
lokraj2003 • 70
• updated
8 weeks ago by
Adrian Pelin • 2.3k
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Comment:
C: Visualizing body organs in R
... Thanks Garan for the link. ...
written 8 months ago by
lokraj2003 • 70
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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
lokraj2003 • 70
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... 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 ...
written 8 months ago by
lokraj2003 • 70
• updated
8 months ago by
jared.andrews07 • 2.3k
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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
lokraj2003 • 70
Latest awards to lokraj2003
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16 days ago,
created a question with more than 1,000 views.
For Annotation with Prokka or RAST.
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5 weeks ago,
created an answer that has been accepted.
For A: how to appropriately export datasets from R studio in an appropriate style?
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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?
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7 weeks ago,
created a question with more than 1,000 views.
For How to plot heatmap for the matrix for the pairwise comparison of sequence similarity in R ?
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Annotation with Prokka or RAST.
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