User: Chirag Parsania

gravatar for Chirag Parsania
Reputation:
430
Status:
Trusted
Location:
University of Macau
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
2 years, 6 months ago
Email:
c**************@gmail.com

Posts by Chirag Parsania

<prev • 84 results • page 1 of 9 • next >
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Comment: C: How to identify bacteria habitats by taxon id or its name
... Hi Vijay, Good to know this new tool. I don't have NGS reads from bacteria. But I found a very useful resource which can fulfil my purpose. [JGI][1] has very rich microbiome annotations. I can easily map taxonomy to ecosystem and habitats. Cheers [1]: https://img.jgi.doe.gov/cgi-bin/m/main.cgi ...
written 3 months ago by Chirag Parsania430
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Comment: C: How to identify bacteria habitats by taxon id or its name
... Hi, I have some blast results of protein from yeast. I got some significant blast hits from the bacteria. I suspect those are probably horizontally transffered genes (HTG) from bacteria to yeast. I quickly want to check habitats of those bacteria to see if yeast habitats and bacterial habitats are ...
written 3 months ago by Chirag Parsania430
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How to identify bacteria habitats by taxon id or its name
... I have list of bacterial species with names and taxonomy id. I want to know their habitats for e.g. human gut, environment, mud etc etc. I don't have any clue how to move on. Any help would be appreciated. Thanks ...
bacteria habitats ecology written 3 months ago by Chirag Parsania430 • updated 3 months ago by 5heikki7.0k
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Comment: C: ggscatter two color issue
... I don't know your data format. See the example below I created from sample data. You can replicate accordingly. Provide output of `head(data1)` to generate for your data. library("ggplot2") library(ggpubr) data <- mpg ggscatter(data,"cty","hwy",col="trans") ...
written 5 months ago by Chirag Parsania430
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Answer: C: ggscatter two color issue
... This is because you provided color twice. Can not provide same argument multiple time ...
written 5 months ago by Chirag Parsania430
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Answer: A: Computing 1Gc 2GC 3GC on any CDS
... Here is the R function to calculate GC, GC1 ,GC2 or GC3. it takes fasta file as input and choice of function (GC/GC1/GC2/GC3). It will return a vector with GC of each sequence library("seqinr") library("Biostrings") getGC <- function(fastaFile , choice = "GC"){ f ...
written 5 months ago by Chirag Parsania430
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Comment: C: Automatic functional annotation of protein sequences
... There is software called [blast2go][1] which performs blast and then subsequent annotation for given set of sequences. [1]: https://www.blast2go.com ...
written 5 months ago by Chirag Parsania430
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Comment: C: topGO: GO terms but no P-value score
... You can do reverse. First do enrichment and then check if you get enriched terms which you are looking for Following are the three main functions I run for topGO to get enriched go term with pvalue. Go through [tutorial][1] to get details of how to create GOdata object ## prepare master obj ...
written 5 months ago by Chirag Parsania430
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Answer: A: How to interpret phylogenetic Dendrogram
... Use this [powerful online tool][1] to create phylogenetic tree. You can select nodes from where you want to collapse tree. There are also various options available to make visualisation better. If you have ncbi ids, you can submit job to [itol][1] from [phylot][2] [1]: http://itol.embl.de [2]: ...
written 5 months ago by Chirag Parsania430
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Comment: C: local blastp against NR database
... Hi genomax, I am the only one using this server. So that is more surprising to me. Though load balance is there cpu usage is very less. One thing I have noticed is as soon as I run program it shows full cpu usage for some time(Till it throws first output). After that cpu usage goes down and never ...
written 5 months ago by Chirag Parsania430

Latest awards to Chirag Parsania

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Student 4 months ago, asked a question with at least 3 up-votes. For How to find intron co-ordinates from the gff file?
Scholar 5 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 6 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Popular Question 6 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Scholar 6 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Popular Question 7 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Popular Question 17 months ago, created a question with more than 1,000 views. For Z-Score calculation by heatmap.2

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