User: saadleeshehreen

Reputation:
70
Status:
Trusted
Location:
Last seen:
3 months, 1 week ago
Joined:
1 year, 7 months ago
Email:
s**************@gmail.com

Posts by saadleeshehreen

<prev • 83 results • page 1 of 9 • next >
0
votes
1
answer
148
views
1
answer
Retrieving organism name
... Hi, I usually use the following command to get GCF_id (Accession) from the NCBI. How Can I retrieve the "organism name/source" from NCBI? cat NZ_id.txt | while read i; do elink -db nuccore -id $i -target assembly|esummary| xtract -pattern DocumentSummary -element AssemblyAccession ; done ...
ncbi assembly e-utlilities written 3 months ago by saadleeshehreen70 • updated 3 months ago by SMK1.9k
0
votes
1
answer
184
views
1
answer
How to Deduplicate files
... Hi, I have list of 160111 protein files. Some of the files are duplication as GCA and GCF id contains same protein sequnces. How I can deduplicate the list on the basis of ASM102201v1? Enterobacter_hormaechei-158836#GCA_001022015.1/GCA_001022015.1_ASM102201v1_protein.faa Enterobacte ...
sequence written 5 months ago by saadleeshehreen70 • updated 5 months ago by finswimmer12k
0
votes
0
answers
179
views
0
answers
How to retrieve "Assembly statistics" for all (~4200) Pseudomonas aeruginosa genome from NCBI?
... Is any script/ source available to get genome size of all published Psedubomonas aeruginosa genomes from NCBI? This information is written in "Assembly statistics" Cheers ...
genome written 6 months ago by saadleeshehreen70
0
votes
0
answers
212
views
0
answers
How to solve the elink error ?
... Hi I am trying to get assembly number ( for example GCF_001166025.1 is for NZ_CQEB01000017.1) for 100 genomes with the following command. The command previously work for me but today giving some error. Anyone know what happen? elink -db nuccore -id NZ_CQEB01000017.1 -target assembly|esum ...
ncbi elink written 7 months ago by saadleeshehreen70
0
votes
2
answers
308
views
2
answers
How to fetch sequences from Proteinortho5 output containing all test species and no duplication in each genome
... Hi, I want to construct a phylogenic tree on 100 *Pseudomonas aeruginosa* genomes. Before constructing the tree, I want to first cluster those genomes on the basis of homology and for this purpose, I am using ProteinOrtho5 software. After running the software with synteny option I want to extract pr ...
proteinortho5 written 9 months ago by saadleeshehreen70 • updated 3 months ago by AlishaQ0
3
votes
2
answers
1.3k
views
5 follow
2
answers
Counting base and nucleotide frequency of multifasta file
... Hi, I have a mulifasta with 2000 sequences. The file is like this. >spacer_1 ATCCCGGGGGGTTTA............... >spacer_2 TCAGGTTT....... . . I want to count how many bases for each of them and what is the frequency of nucleotide (A,T,G,C) in each of the sequence. I tried ...
multifasta base count nucleotide frequency written 10 months ago by saadleeshehreen70 • updated 10 months ago by Firas0
0
votes
0
answers
344
views
0
answers
Comment: C: Problem to run a perl script from shell
... same error message is showing ...
written 10 months ago by saadleeshehreen70
3
votes
0
answers
344
views
6 follow
0
answers
(Closed) Problem to run a perl script from shell
... Hi, why the error is given though the file is here -bash-4.2$ ls fna_PA.ls resfinder.pl tmp -bash-4.2$ perl resfinder.pl Error: No such file or directory How to solve the problem? ...
perl written 10 months ago by saadleeshehreen70
0
votes
0
answers
417
views
0
answers
Comment: C: How to install CRISPRdisco
... Thanks for suggestions. I have contacted them and waiting for the response. ...
written 10 months ago by saadleeshehreen70
2
votes
0
answers
417
views
0
answers
How to install CRISPRdisco
... I am trying to install the software on our server (https://github.com/CRISPRlab/CRISPRdisco ). I have no root permission to install any software and I am unfamiliar with docker. So, I tried to follow the instruction written under **To install by hand** to install the software. While trying to run wi ...
docker written 10 months ago by saadleeshehreen70 • updated 10 months ago by Michael Dondrup46k

Latest awards to saadleeshehreen

Popular Question 5 months ago, created a question with more than 1,000 views. For grep things and counting line number in R
Popular Question 9 months ago, created a question with more than 1,000 views. For grep things and counting line number in R

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1609 users visited in the last hour