WHAT OUTPUT FILE I NEED USE?

Luciano C. Maia

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Feb 14, 2018, 9:35:17 AM2/14/18

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Congratulations!

Please, I start working with trans-abyss just now...
When I use the command;
transabyss --pe reads1.fq reads2.fq -k 25 --outdir assembly25

I have this files em my directory. My questions is: What file I use to final analisys?

assembly25-1.adj
assembly25-1.fa
assembly25-3.adj
assembly25-3.dist
assembly25-3.fa
assembly25-3.hist
assembly25-4.adj
assembly25-4.fa
assembly25-4.path1
assembly25-4.path2
assembly25-4.path3
assembly25-5.adj
assembly25-5.fa
assembly25-5.path
assembly25-6.fa
assembly25-bubbles.fa
assembly25.CONTIGS.COMPLETE
assembly25.DBG.COMPLETE
assembly25.FINAL.COMPLETE
assembly25-final.fa
assembly25-jn.fa
assembly25-jn.path
assembly25.JUNCTIONS.COMPLETE
assembly25.REFERENCES.COMPLETE
assembly25-ref.fa
assembly25-ref.path
assembly25.UNITIGS.COMPLETE

Thanks!
Luciano Maia

Ka Ming Nip

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Feb 14, 2018, 12:23:45 PM2/14/18

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Hi,

Your final output file from Trans-ABySS is `assembly25-final.fa`

Ka Ming

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Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
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Subject: WHAT OUTPUT FILE I NEED USE?

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Luciano C. Maia

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Feb 14, 2018, 12:27:02 PM2/14/18

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николай шмаков

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May 26, 2018, 2:05:06 AM5/26/18

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Dear Ka Ming,

Thank you very much for the explanation,
but could you please be so kind to elaborate - what are the other files that Trans-ABySS outputs? *-1.fa and *-3.fa must be temporary files? and what are files -jn.fa , -ref.fa and -bubbles.fa ? what contigs do they store?

thank you

Nickolay Shmakov

четверг, 15 февраля 2018 г., 0:23:45 UTC+7 пользователь Ka Ming Nip написал:

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Ka Ming Nip

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May 28, 2018, 2:51:10 AM5/28/18

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These are all temporary files from different stages of the assembly.
If you use the `--cleanup 3` option, they would all be removed.

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________

From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of николай шмаков [deatha...@gmail.com]
Sent: May 25, 2018 11:05 PM
To: Trans-ABySS
Subject: Re: WHAT OUTPUT FILE I NEED USE?

Dear Ka Ming,
Thank you very much for the explanation,
but could you please be so kind to elaborate - what are the other files that Trans-ABySS outputs? *-1.fa and *-3.fa must be temporary files? and what are files -jn.fa , -ref.fa and -bubbles.fa ? what contigs do they store?
thank you

Nickolay Shmakov

четверг, 15 февраля 2018 г., 0:23:45 UTC+7 пользователь Ka Ming Nip написал:
Hi,

Your final output file from Trans-ABySS is `assembly25-final.fa`

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________

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николай шмаков

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May 30, 2018, 7:14:21 AM5/30/18

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I see, thank you very much

понедельник, 28 мая 2018 г., 13:51:10 UTC+7 пользователь Ka Ming Nip написал:

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