How to merge mfasta of each reference

[tomitaMDU]

Hi David,

I concatenated 1 chromosome and 6 plasmids to one ref but I getting total 7 mfasta files. I wnat to merge them into one mfasta, how can I do it? and there is no SNPs difference table. Do you know why?

Can you have a look at your convinience? /hsm/VR0082/shared/MDU/pipe_out/RedDog_output/VREAUS0085-140721

Tomi

[schultzm]

Hi Tomi,

Try this on the command line

"cat 1.mfasta 2.masta … 7.mfasta > allmfastascombined.mfasta"

Note, that this does not mean the sequences will be aligned.

Cheers,

Mark

From: tomitaMDU notifications@github.com<mailto:notifications@github.com> Reply-To: katholt/RedDog reply@reply.github.com<mailto:reply@reply.github.com> Date: Wednesday, 23 July 2014 12:45 PM To: katholt/RedDog RedDog@noreply.github.com<mailto:RedDog@noreply.github.com> Subject: [RedDog] How to merge mfasta of each reference (#18)

Hi David,

I concatenated 1 chromosome and 6 plasmids to one ref but I getting total 7 mfasta files. I wnat to merge them into one mfasta, how can I do it? and there is no SNPs difference table. Do you know why?

Can you have a look at your convinience? /hsm/VR0082/shared/MDU/pipe_out/RedDog_output/VREAUS0085-140721

Tomi

— Reply to this email directly or view it on GitHubhttps://github.com/katholt/RedDog/issues/18.

[d-j-e]

Hi Tomi,

each sequence (replicon) in the multi-sequence Genbank is reported separately. So for each genome and plasmid there is a separate SNP difference table.

Given you have so few sequences you could open each and concatenate them in a text editor - however, plasmids may well have a different phylogenetic history than the genomes (or each other), so concatenating them could confuse the phylogenetic signals. Also, you need to look at the plasmids to see which is/are actually present (some may share genes, hence reads from one plasmid will map to the other...)

cheers, David

[tomitaMDU]

Hi Mark,

I will try. Thank you very much.

Best regards,

Takehiro Tomita, PhD

Molecular Scientist

Microbiological Diagnostic Unit - Public Health Laboratory Department of Microbiology & Immunology Peter Doherty Institute for Infection and Immunity The University Of Melbourne

Address: Level 1,792 Elizabeth Street (Corner of Grattan & Elizabeth Streets) Melbourne 3010 Department of Microbiology & Immunology The University of Melbourne – Enter Foyer and take a lift to Level 1.

Phone 1:+61 3 83445713 Phone 2:+61 3 83445701 Fax: +61 3 83447833

From: schultzm [mailto:notifications@github.com] Sent: Wednesday, 23 July 2014 12:50 PM To: katholt/RedDog Cc: Takehiro Tomita Subject: Re: [RedDog] How to merge mfasta of each reference (#18)

Hi Tomi,

Try this on the command line

"cat 1.mfasta 2.masta … 7.mfasta > allmfastascombined.mfasta"

Note, that this does not mean the sequences will be aligned.

Cheers,

Mark

From: tomitaMDU notifications@github.com<mailto:notifications@github.com> Reply-To: katholt/RedDog reply@reply.github.com<mailto:reply@reply.github.com> Date: Wednesday, 23 July 2014 12:45 PM To: katholt/RedDog RedDog@noreply.github.com<mailto:RedDog@noreply.github.com> Subject: [RedDog] How to merge mfasta of each reference (#18)

Hi David,

I concatenated 1 chromosome and 6 plasmids to one ref but I getting total 7 mfasta files. I wnat to merge them into one mfasta, how can I do it? and there is no SNPs difference table. Do you know why?

Can you have a look at your convinience? /hsm/VR0082/shared/MDU/pipe_out/RedDog_output/VREAUS0085-140721

Tomi

— Reply to this email directly or view it on GitHubhttps://github.com/katholt/RedDog/issues/18.

— Reply to this email directly or view it on GitHubhttps://github.com/katholt/RedDog/issues/18#issuecomment-49827315.