User: Chirag Parsania

gravatar for Chirag Parsania
Reputation:
420
Status:
Trusted
Location:
University of Macau
Scholar ID:
Google Scholar Page
Last seen:
19 hours ago
Joined:
2 years, 1 month ago
Email:
c**************@gmail.com

Posts by Chirag Parsania

<prev • 81 results • page 1 of 9 • next >
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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 23 hours ago by Chirag Parsania420
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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 1 day ago by Chirag Parsania420
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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 3 days ago by Chirag Parsania420
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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 3 days ago by Chirag Parsania420
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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 11 days ago by Chirag Parsania420
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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 11 days ago by Chirag Parsania420
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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 13 days ago by Chirag Parsania420
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Comment: C: local blastp against NR database
... Hi @genomax, Does it affect a lot in terms of timing to get first output of blastp if we increase `-max_target_seqs 1000` ? Because I am running blastp with 10 threads and it's more than 12 hrs, no output yet. Second, see the output of top command [here][1]. Though `blastp` is running cpu usage i ...
written 14 days ago by Chirag Parsania420
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Comment: A: local blastp against NR database
... Hi Vijay, Thanks for providing useful link. It was quite surprising that I didn't get any output after 24 hrs. Unfortunately it was true. I tried to figure out the reason and this is what I understood. I ran 270 independent blastp commands each with 1 thread (`--num_threads 1`). Here, the problem ...
written 16 days ago by Chirag Parsania420
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local blastp against NR database
... Hi, I am running blastp programme locally against NR database. I have 272 threads in total (68 * 4). To use all computational resources I split my query fasta file in the 270 files and running blastp simultaneously on all 270 files against NR database. In blast command for `--num_threads` i am usin ...
nr blastp time written 16 days ago by Chirag Parsania420

Latest awards to Chirag Parsania

Scholar 11 days ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 4 weeks ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Scholar 5 weeks ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Good Answer 8 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 8 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 12 months ago, created a question with more than 1,000 views. For Z-Score calculation by heatmap.2

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