User: Freddy

gravatar for Freddy
Freddy20
Reputation:
20
Status:
New User
Location:
Last seen:
4 weeks ago
Joined:
8 months, 2 weeks ago
Email:
F**********@gmail.com

Posts by Freddy

<prev • 15 results • page 1 of 2 • next >
1
vote
1
answer
124
views
1
answer
Finding the centromere and telomere of cattle genome (Bos Taurus)
... Does anyone know how I can get the coordinates of the centromere and telomere of a chromosome of reference cattle(Bos Taurus) genome using online tools like NCBI? I have searched a lot, but I could not find anything useful. Based on my findings, wet lab analysis is required to locate the centromer ...
ncbi genome cattle centromere chromosome written 3 months ago by Freddy20 • updated 3 months ago by antonioggsousa1.5k
9
votes
3
answers
178
views
7 follow
3
answers
Parsing a portion of a fasta file header
... I have a big fasta file, which contains multiple headers followed by sequences. A small part of the file is shown below: >XP_024503355.1 Integrator complex subunit 11 [Strongyloides ratti] >CEF64154.1 Integrator complex subunit 11 [Strongyloides ratti] MKIVCLGAGCDVGRSCILLKIGNKRVMLDCGI ...
fasta bash parse terminal linux written 5 months ago by Freddy20 • updated 5 months ago by Mensur Dlakic6.9k
0
votes
2
answers
227
views
2
answers
Comment: C: how to find the kingdom for a taxon id using the terminal?
... Thank you so much! I have been searching for an answer quite a while, but haven't managed to find anything. It tried your solution and it works perfectly, thank you so much. May I ask you where you have learned details like this? ...
written 6 months ago by Freddy20
0
votes
2
answers
227
views
2
answers
Comment: C: how to find the kingdom for a taxon id using the terminal?
... I have trying to search for the taxonomy division of multiple taxids using the following in R: taxid <- c(7070, 5741, 658858) taxid.as.string <- paste(taxid,collapse=", ") batch <- system(paste0("esearch -db taxonomy -query \"",taxid.as.string, " [taxID]\" | efetch -format xml | xtract ...
written 6 months ago by Freddy20
0
votes
1
answer
219
views
1
answers
Comment: C: system() command in R does not return output in order
... I do not want to run this query line by line for every single taxid as it takes a lot of time, that is why I was making queries in batches. Do you how I can include the taxids in the results? By adding TaxId to the -element, I will get the taxid for every single taxonomy division, but I only want t ...
written 6 months ago by Freddy20
4
votes
1
answer
219
views
1
answer
system() command in R does not return output in order
... I am trying to access the `NCBI` database from R, where I pass on a system command within R using `system(..., intern = T)` and return the result back into a variable. The command is a query which retrieves the taxonomy, given a `taxID`. It looks like the following: ``` batch <- system(paste0("e ...
ncbi R command-line written 6 months ago by Freddy20
0
votes
2
answers
227
views
2
answers
Comment: C: how to find the kingdom for a taxon id using the terminal?
... Interestingly, this command does not work for the ones which don't have the kingdom in their lineage. my intention is to get the kingdom for as many as taxon ID possible, and kingdom is not there, I will get either phylum or anything that is found after kingdom. this is an example: esearch -db taxon ...
written 7 months ago by Freddy20
0
votes
2
answers
227
views
2
answers
Comment: C: how to find the kingdom for a taxon id using the terminal?
... Thank you very much, May I ask how I can change this command to for example get the phylum? ...
written 7 months ago by Freddy20
7
votes
2
answers
227
views
2
answers
how to find the kingdom for a taxon id using the terminal?
... I need to find the kingdom for some taxon IDs. I am already using the following Entrez command to get the full taxonomy for a specific taxon ID. esearch -db taxonomy -query "4932 [taxID]" | efetch -format nativemode xml | xtract -pattern Taxon -block "*/Taxon" -unless Rank -equals "no rank" -t ...
ncbi kingdom taxonomy terminal written 7 months ago by Freddy20 • updated 7 months ago by genomax91k
0
votes
2
answers
346
views
2
answers
Comment: C: converting taxID to taxonomy
... @genomax Thank you very much, it works perfectly. There is a manual on how to use Entrez on NCBI, but I find it difficult to use. Do you have any suggestions for me on how to learn Entrez' commands properly? ...
written 7 months ago by Freddy20

Latest awards to Freddy

Supporter 28 days ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2218 users visited in the last hour