User: Nitin Narwade

gravatar for Nitin Narwade
Nitin Narwade420
Reputation:
420
Status:
Trusted
Location:
India
Last seen:
20 hours ago
Joined:
2 years, 11 months ago
Email:
n***************@gmail.com

Posts by Nitin Narwade

<prev • 87 results • page 1 of 9 • next >
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Comment: C: Genome assembly statistical tools
... You just have to google it and you will find the number of options out there. Like I did and found quast. ...
written 13 days ago by Nitin Narwade420
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Comment: C: reading gse series matrix data
... There is no expression data in the series matrix of **GSE79362**. For this example, I have used **GSE2553** GEO id and code will be something like this. gse <- getGEO(filename="GSE2553_series_matrix.txt.gz",GSEMatrix = TRUE,getGPL = FALSE) #Retrieve matrix data and store it in R object ...
written 28 days ago by Nitin Narwade420
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Comment: C: reading gse series matrix data
... I think you should look at GEOparse, it may help you. I do not have any experience working with GEOparse, but I have used GEOquery (an R package, which is base for GEOparse) which will read GSE Series Matrix. ...
written 29 days ago by Nitin Narwade420
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Comment: C: Extracting uniquely mapped reads from bams
... I think [this biostars thread][1] might be helpful in your case. [1]: https://www.biostars.org/p/56246/ ...
written 12 weeks ago by Nitin Narwade420
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Comment: C: Sort genomes for gene presence
... You can use searching gene against genome strategy using blast+ (blastn - searches nucleotide gene sequence against genome database) utility. But searching a gene sequence against predicted genes is a good strategy and would be more precise than searching against genome. You can use `.fasta` file ...
written 5 months ago by Nitin Narwade420
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Comment: C: De novo Genome Sequence
... could you explain your question little wider, in terms of what kind of organism it is, what you're going to achieve and all? One more thing what does it mean **genome sequencing of an organism without knowing the genome size?**. ...
written 7 months ago by Nitin Narwade420
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Comment: C: Genome annotation using COG
... What is the organism your working on and what would be the approximate genome size? Let's consider average genome size for your organism is 7.5-8Mb. Then your assembly is good. If it is 5Mb then there is likely to have contamination for sure. Thank you. ...
written 7 months ago by Nitin Narwade420
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Comment: C: How to separate sequences of two species from Metagenomics Analysis?
... Dear hafiz.talhamalik, If my suggestion somehow helps you to get an idea for resolving your query, could you please hit on upvote button? Thank you. ...
written 7 months ago by Nitin Narwade420
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Comment: C: loop several conditions R
... If your file name vectors always have the same length then there is no need of nested loop, the single loop should work. for example: metaxcan <- c("foo1.csv", "foo2.csv") predix_asso <- c("soo1.csv", "soo2.csv") for (i in c(1:length(metaxcan)) { PGC<-read.csv(metaxc ...
written 7 months ago by Nitin Narwade420
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Comment: C: Kaiju or MetaPhlAn2?
... I think you can not rely on a single tool, in this case, I would suggest you can use multiple tools and check the results and then decide. Because the problem for all these tools (`Kaiju, MetaPhlAn2 or Kraken`) is, all of them will assign taxonomy on the basis of reference dataset. I think MetaPhl ...
written 7 months ago by Nitin Narwade420

Latest awards to Nitin Narwade

Popular Question 5 months ago, created a question with more than 1,000 views. For how to filter ChIP-Seq peaks called by MACS based on the measurements?
Scholar 9 months ago, created an answer that has been accepted. For A: about bioperl script for extracting sequences from a fasta file(get orf output f
Scholar 10 months ago, created an answer that has been accepted. For A: about bioperl script for extracting sequences from a fasta file(get orf output f
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: about bioperl script for extracting sequences from a fasta file(get orf output f

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