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435

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Visualising Roary Results

genome sequence alignment roary snp written 7 months ago by Fid_o • 20 • updated 11 days ago by herber4 • 0

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127

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How to upload accessory_binary_genes.fa.newick and gene_presence_absence.csv files in Phandango?

software error python roary snp bioinformatics written 29 days ago by Dineshkumar K • 40

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181

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Unique genes roary

comparative genomics pangenome roary written 6 weeks ago by Sissi • 50

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116

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How to obtain compile core gene sequences from Roary?

pangenomics roary core genes written 11 weeks ago by ethanfoo360 • 0

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264

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Ways to convert fasta to faa file for functional annotation?

assembly pangenome roary annotation written 6 months ago by c.e.chong • 20 • updated 6 months ago by Biostar ♦♦ 20

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236

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inconsistent pan genome results with roary

genome pangenome roary written 8 months ago by elenaf • 0

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634

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Roary producing erroneous plots?

R roary written 18 months ago by Lesley Sitter • 540 • updated 18 months ago by Joe ♦ 18k

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3.3k

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Converting .fasta files to .gff3 files

fasta gff3 roary written 3.8 years ago by chenbenyuan • 0 • updated 3.5 years ago by Biostar ♦♦ 20

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1.7k

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Roary pan genome analysis: where can I find 'clustered_proteins' for the command Roary query_pan_genome -a union -g clustered_proteins *.gff

pangenome roary pan-genome written 4.6 years ago by daniel.knight • 10 • updated 4.5 years ago by mah2002 • 10

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2.5k

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Roary pan genome analysis error

pangenome roary written 4.6 years ago by jeccy.J • 50

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Recent Replies

C: Way to check if gene A lies in the same ORF as gene B by i.sudbery ♦ 9.4k
Open reading frames are part of genes, not vice-versa. You cannot have two genes that are part of...
C: BWA mem minimum read length by yolek64754 • 10
Thanks for the quick answer. Yeah I don't use them in my analysis, I was just curious of why some...
C: Read DNA sequence from FASTA rising a subclass? by Ionic_Bond • 0
Thank so much for your help. I will look at it carefully once I get back home after work :)
C: Individual genes plots after batch correction with Deseq2 by Eugene A • 80
matrix - is either count matrix or Deseq object - if later is true - set deseq_res = True row - ...
C: BWA mem minimum read length by ATpoint ♦ 40k
There is no hard cutoff in the code afaik. It is probably a combination of the alignment score wi...
C: Attempt to set 'rownames' on an object with no dimensions by ks.sholohova • 0
Thank you very much, Andres! Now everything perfectly works. I just want to make sure please tha...
A: How can I know when a pathway was included in Reactome? by darklings • 90
2020: Try the [`ReactomeContentService4R`](https://github.com/reactome/ReactomeContentService4R) ...
C: Read DNA sequence from FASTA rising a subclass? by Fatima • 740
Hi! Is this the script that you use? If so, the def check part should be moved to the top. Also...
C: Converting VCF files into bcftools style region co-ordinates by Pierre Lindenbaum ♦ 131k
I do not understand
C: Blastpcmd (Windows) - Too Many Positional Arguments by genomax ♦ 91k
You can accept the answers below (green check mark) to provide closure to this thread. You can ac...
A: Attempt to set 'rownames' on an object with no dimensions by andres.firrincieli • 960
Try this: rownames(SpiecEasi.matrix$refit$stars) <- colnames(amgut1.filt)
A: Blastpcmd (Windows) - Too Many Positional Arguments by wwaner26 • 0
Thank you all. When I recreate the `db`, everything goes all right.

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