User: Chirag Parsania
Chirag Parsania • 430
- Reputation:
- 430
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- Trusted
- Location:
- University of Macau
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- Google Scholar Page
- Last seen:
- 1 week, 6 days ago
- Joined:
- 2 years, 9 months ago
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Posts by Chirag Parsania
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Comment:
C: blastdbcmd taxonomy id conflict
... Hi lieven, Thanks for this. By the way got same reply from NCBI. See below
__________________________________________________________________
**You may want to update the metadata file by redownload the taxdb.tar.gz file from our ftp site as well as update your nr or refseq_protein database.
Worki ...
written 11 weeks ago by
Chirag Parsania • 430
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Comment:
C: blastdbcmd taxonomy id conflict
... Hi Sterk, you have changed the input id from WP_071944094.1 to WP_053947656.1. There is no issue with WP_053947656.1.
I ran the same command with my database version (perhaps mine is little older than you. Downloaded in mid 2017). It gave me same output like yours.
WP_053947656.1 928922717 ...
written 12 weeks ago by
Chirag Parsania • 430
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Comment:
C: blastdbcmd taxonomy id conflict
... Hi, I believe you said it rightly. I found below paragraph form the link you shared, which explains the cause for the question I asked.
**A non-redundant protein record that provides organism information at the level of a genus, family, or even super-kingdom does not mean that the protein is found ...
written 12 weeks ago by
Chirag Parsania • 430
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... Hi,
I am using 'blastdbcmd ' command to map taxonomy ids and other details to the local blast outcomes. For the query protein “**WP_071944094.1**” I found taxonomy id conflict between what I get locally and online record. See the command and outcome given below for your reference.
**Local command ...
written 12 weeks ago by
Chirag Parsania • 430
• updated
12 weeks ago by
lieven.sterck • 1.2k
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... 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 6 months ago by
Chirag Parsania • 430
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... 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 6 months ago by
Chirag Parsania • 430
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... 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
...
written 6 months ago by
Chirag Parsania • 430
• updated
6 months ago by
5heikki ♦ 7.2k
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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 8 months ago by
Chirag Parsania • 430
1
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1
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564
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1
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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 8 months ago by
Chirag Parsania • 430
1
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2
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... 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 8 months ago by
Chirag Parsania • 430
Latest awards to Chirag Parsania
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5 months ago,
created a question with more than 1,000 views.
For Extract reads from bam/sam files using read id
Student
7 months ago,
asked a question with at least 3 up-votes.
For How to find intron co-ordinates from the gff file?
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8 months ago,
created an answer that has been accepted.
For A: GO enrichment - interpreting broad terms
Scholar
9 months ago,
created an answer that has been accepted.
For A: GO enrichment - interpreting broad terms
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9 months ago,
created a question with more than 1,000 views.
For Extract reads from bam/sam files using read id
Scholar
9 months ago,
created an answer that has been accepted.
For A: GO enrichment - interpreting broad terms
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10 months ago,
created a question with more than 1,000 views.
For Extract reads from bam/sam files using read id
Good Answer
17 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
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17 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
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17 months ago,
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For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
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