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How can I analyze and compare the core genome of several organisms?

genome core genome alignment written 21 months ago by Airam • 0 • updated 20 months ago by Carambakaracho • 1.9k

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670

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Who has tried bcgTree - Comments?

phylogeny core genome aligment written 2.9 years ago by mschmid • 110

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1.7k

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Pan and core Genome prediction from OrthoMCL output

core genome pangenome orthomcl mcl written 3.0 years ago by akhilvbioinfo • 140 • updated 3.0 years ago by Joe ♦ 16k

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2.3k

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Split fasta file into chromosomes

fasta core genome contigs chromosome written 3.8 years ago by natasha • 100

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2.6k

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Processing OrthoMCL output file, "groups.txt" to create a venn diagram

orthologs core genome genome comparison orthomcl written 4.9 years ago by jc_0919 • 0

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Recent Replies

A: Problem running QUAST assembly evaluation: quast tries to write to read-only FS by tospo • 40
Thanks for all the comments, it works now! The solution was indeed to install minimap2 which I...
C: Trimming out primer sequences in the middle of reads by ricardoguerreiro2121 • 30
Hello, does your script also remove the reverse complement? Do I find it within the BBmap scripts?
A: Cytoscape: is there a way to export selected sequences into a fasta file? by scooter • 140
Indeed, we do monitor Biostars :-) Where are you getting your sequence similarity network? If t...
C: [cph] Error in `[.default`(y, , 3) : subscript out of bounds by russhh • 5.0k
find out what is throwing the error: use debug(cph) , then make your cph call as above, and step ...
C: Running BWA mem in a for loop by Joe ♦ 16k
I haven't tested it but you could simply capture the output. The shell should deal with all the v...
A: Homer error, how to call homer properly in a script? and how to know that it's a by Ankur B. Sharma • 10
You should open the findMotifsGenome.pl script and change the path to homer in your system. Hope ...
A: What should be reported as Hazard Ratio in Kaplan Meier curve? by huynguyen96.dnu • 0
Sorry, but I have a question on the interpretation of HR value. According to your above result, H...
A: Running BWA mem in a for loop by Giovanni.madrigal12 • 130
You can do something like `for i in $(ls -1 *R1.fq.gz | sed 's/\.R1.fq.gz//'); do bwa mem -t 16...
C: How To Update R In Ubuntu ? by gabrielhg88 • 0
Made it work by deleting everything related to R first rm -rf /usr/local/lib/R I then used ...
C: [cph] Error in `[.default`(y, , 3) : subscript out of bounds by huynguyen96.dnu • 0
mod.cox <- cph(formula(Surv(OS_MONTHS, OS_STATUS) ~ CELLULARITY + MENOPAUSAL_STATE + ER_S...
A: Consecutive Window Rna Folding by jtimmons • 30
Hello. Reviving another close-for-a-bit BioStars thread to share that I made a DNA/RNA folding li...
C: There are any way to use a script for feed emboss with fasta sequence? by schlogl • 50
Thanks Joe. I appreciate you effort to help. Thank you very much.

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