User: saadleeshehreen

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Posts by saadleeshehreen

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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 7 weeks ago by saadleeshehreen60 • updated 7 weeks ago by finswimmer11k
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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 11 weeks ago by saadleeshehreen60
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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 3 months ago by saadleeshehreen60
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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 6 months ago by saadleeshehreen60 • updated 8 hours ago by AlishaQ0
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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 6 months ago by saadleeshehreen60 • updated 6 months ago by Firas0
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Comment: C: Problem to run a perl script from shell
... same error message is showing ...
written 6 months ago by saadleeshehreen60
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(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 6 months ago by saadleeshehreen60
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Comment: C: How to install CRISPRdisco
... Thanks for suggestions. I have contacted them and waiting for the response. ...
written 6 months ago by saadleeshehreen60
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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 6 months ago by saadleeshehreen60 • updated 6 months ago by Michael Dondrup46k
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Install CRISPRCasFinder under Ubuntu without having administrator rights
... Hi, I need to install the following software in our server. https://crisprcas.i2bc.paris-saclay.fr/Home/Download Our server uses linux operating system but I don't have administrator rights. I usually use conda to install any software but this particular one doesn't have conda version. How can I in ...
crispr install linux written 6 months ago by saadleeshehreen60 • updated 6 months ago by WouterDeCoster39k

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Popular Question 6 months ago, created a question with more than 1,000 views. For grep things and counting line number in R

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