User: 3335098459

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333509845920
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Posts by 3335098459

<prev • 35 results • page 1 of 4 • next >
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snippy multi is prompting unreadable files
... Hi, I have tried generating tab file by pasting all the filenames and paths in excel and later converted that csv file using this command. sed -e 's/,/\t/g' input.csv > input2.tab and then ran the following command and this message showed up: root@hon-pc:/home/fan/monas/fna# snippy-mu ...
gene assembly snp written 9 days ago by 333509845920
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Answer: A: Phylogenetic Analysis of gene sequences with Non-synonymous mutations
... Muscle is working fine if run manually and not in MEGA. Thanks anyways ...
written 10 days ago by 333509845920
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generate .tab file for snippy with filenames & paths
... Hi, I have just started learning linux CLI. I am using snippy tool for comparing multiple files that require a .tab format file. This tab formatted file should be consisting of the paths and filenames separated by tab (\t). I have run this two commands separately to generate a list of filenames an ...
genome snp written 10 days ago by 333509845920
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Phylogenetic Analysis of gene sequences with Non-synonymous mutations
... Hello, I have a large number of complete genomes (downloaded from NCBI) related to the same bacterial species. As it is mentioned in the guidelines of MUSCLE, I have already used Usearch for clustering (Uclust) and divided my data to different gene clusters. I have used MEGA software on Windows. Bu ...
genome assembly alignment snp written 27 days ago by 333509845920
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Python script for ATGC count
... Hi, I am new to Python so if this query seems to you a piece of cake. Please I apologize in advance. I have a python script to count ATGC def readGenome(filename): genome = '' with open(filename, 'r') as f: for line in f: # ignore header line with genome information ...
genome software error sequence written 6 weeks ago by 333509845920 • updated 5 weeks ago by antonioggsousa1.4k
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Plasmid and Phage identification package
... Hi, I downloaded around 400 genomes from NCBI. I need to identify phages and plasmids if there is any. Is there any Linux based software that can identify plasmids/phages? Write those phages/plamsid sequences to a new separate file and the chromosomal sequences without plasmid/phages to other new f ...
sequencing written 7 months ago by 333509845920 • updated 7 months ago by onestop_data260
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Comment: C: grep with -f switch is not working
... However, I have used a less algorithmic way. I have replaced all the spaces and tabs with -e and made a long command with all the labels having -e switch, the path to the directory and used grep. It worked fine. But still, I want to figure out this. ...
written 10 months ago by 333509845920
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Comment: C: grep with -f switch is not working
... I don't know. Whenever I entered this command and pressed enter. The cursor moves to the next line but nothing happens. I mean no results are being shown. ...
written 10 months ago by 333509845920
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grep with -f switch is not working
... Hi, I have multiple gene Ids or labels in a file. I want to use grep -f file.txt *.aln to find out in which alignment files my genes are present. I have tried grep --help and the -f switch is mentioned there. But the problem is: this command is not working in my linux system. Could anybody explain ...
grep written 10 months ago by 333509845920 • updated 10 months ago by zx87549.6k
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Comment: C: Recombination location in gubbins output
... Hi, I think you should try PHANDANGO. There are many examples shown according to your demand. ...
written 10 months ago by 333509845920

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