User: Chirag Parsania

gravatar for Chirag Parsania
Reputation:
430
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Trusted
Location:
University of Macau
Scholar ID:
Google Scholar Page
Last seen:
1 week, 6 days ago
Joined:
2 years, 9 months ago
Email:
c**************@gmail.com

Posts by Chirag Parsania

<prev • 88 results • page 1 of 9 • next >
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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 Parsania430
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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 Parsania430
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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 Parsania430
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blastdbcmd taxonomy id conflict
... 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 ...
taxonomyid localblast blastp written 12 weeks ago by Chirag Parsania430 • updated 12 weeks ago by lieven.sterck1.2k
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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 6 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 6 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 6 months ago by Chirag Parsania430 • updated 6 months ago by 5heikki7.2k
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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 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 8 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 8 months ago by Chirag Parsania430

Latest awards to Chirag Parsania

Popular Question 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?
Scholar 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
Popular Question 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
Popular Question 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
Teacher 17 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 20 months ago, created a question with more than 1,000 views. For Z-Score calculation by heatmap.2

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