command setup

[Feng Tao]

Hi, Ka. 

I am new to the bioinformatics area and trying to use transabyss 2.0.1 to do de novo assembly. However, I do not understand how to set up the paired-end sequence. 

My code is like that: 

transabyss --se Phragmites_RNA/combined_read/skewer_all_P1.fq --pe Phragmites_RNA/combined_read/skewer_all_P2.fq --kmer 21 --outdir Phragmites_RNA/transabyss --threads 4

Is this code OK? Or I need to change it to --pe parameter, as 

transabyss --pe Phragmites_RNA/combined_read/skewer_all_P/1.fq Phragmites_RNA/combined_read/skewer_all_P/2.fq --kmer 21 --outdir Phragmites_RNA/transabyss --threads 4

parameter Sorry for any inconvenience. Many thanks! 

[Ka Ming Nip]

Hi Feng,

The 2nd command is correct.

Ka Ming

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

---

From: trans...@googlegroups.com <trans...@googlegroups.com> on behalf of Feng Tao <toby...@gmail.com>
Sent: October 7, 2019 12:54 PM
To: Trans-ABySS
Subject: command setup

 

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[Feng Tao]

Thanks for your reply, Ka. 

Can file be named Phragmites_RNA/combined_read/skewer_all_P/1.fq? Or the file end with 1 or 2, like Phragmites_RNA/combined_read/skewer_all_P1.fq? 

Many thanks! 

On Monday, 7 October 2019 16:10:04 UTC-4, Ka Ming Nip wrote:

Hi Feng,

The 2nd command is correct.

Ka Ming

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

---

From: trans...@googlegroups.com <trans...@googlegroups.com> on behalf of Feng Tao <toby...@gmail.com>
Sent: October 7, 2019 12:54 PM
To: Trans-ABySS
Subject: command setup

 

Hi, Ka. 

I am new to the bioinformatics area and trying to use transabyss 2.0.1 to do de novo assembly. However, I do not understand how to set up the paired-end sequence. 

My code is like that: 

transabyss --se Phragmites_RNA/combined_read/skewer_all_P1.fq --pe Phragmites_RNA/combined_read/skewer_all_P2.fq --kmer 21 --outdir Phragmites_RNA/transabyss --threads 4

Is this code OK? Or I need to change it to --pe parameter, as 

transabyss --pe Phragmites_RNA/combined_read/skewer_all_P/1.fq Phragmites_RNA/combined_read/skewer_all_P/2.fq --kmer 21 --outdir Phragmites_RNA/transabyss --threads 4

parameter Sorry for any inconvenience. Many thanks! 

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[Ka Ming Nip]

​You can name the read files anyway you want as long as the constituent read names matches for each pair of files.

Ka Ming

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

From: trans...@googlegroups.com <trans...@googlegroups.com> on behalf of Feng Tao <toby...@gmail.com>

Sent: October 7, 2019 1:16 PM
To: Trans-ABySS
Subject: Re: command setup

 

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