User: Chirag Parsania
Chirag Parsania • 420
- 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 >
0
votes
1
answer
182
views
1
answers
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 Parsania • 420
1
vote
1
answer
182
views
1
answers
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 Parsania • 420
1
vote
2
answers
130
views
2
answers
... 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 Parsania • 420
1
vote
1
answer
127
views
1
answers
... 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 Parsania • 420
1
vote
0
answers
135
views
0
answers
... 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 Parsania • 420
2
votes
1
answer
185
views
1
answers
... 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 Parsania • 420
0
votes
1
answer
374
views
1
answers
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 Parsania • 420
0
votes
1
answer
374
views
1
answers
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 Parsania • 420
0
votes
1
answer
374
views
1
answers
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 Parsania • 420
5
votes
1
answer
374
views
1
answer
... 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 ...
written 16 days ago by
Chirag Parsania • 420
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
Appreciated
8 months ago,
created a post with more than 5 votes.
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 496 users visited in the last hour