Correct specification of paired-end reads

[winni2k]

This is just a question to make sure I understood the README.md correctly. If I want to assemble regular paired-end reads stored in separate files (not strand-specific), then the correct way to do that is with this command?

transabyss --se forward.fq.gz reverse.fq.gz --pe forward.fq.gz reverse.fq.gz

[sjackman]

@kmnip @readmanchiu I looked in sample_dataset/assemble.sh for an example. It uses --se. Should that be --pe?

https://github.com/bcgsc/transabyss/blob/05e0b2ca5fe241891be308279d43aabe3311fd57/sample_dataset/assemble.sh#L23-L26

[sjackman]

@winni2k I believe that

transabyss --se forward.fq.gz reverse.fq.gz --pe forward.fq.gz reverse.fq.gz

and

transabyss --pe forward.fq.gz reverse.fq.gz

are equivalent. I'd be inclined to use the latter. Ka Ming or Readman can confirm.

https://github.com/bcgsc/transabyss/blob/master/TUTORIAL.md#13-input-reads

[kmnip]

@winni2k , you only need to use the --pe option for pair-end RNA-seq data, eg.

transabyss --pe forward.fq.gz reverse.fq.gz

If you have more than one set of paired-end read files (eg. libraries "A" and "B"), then:

transabyss --pe libraryA_forward.fq.gz libraryA_reverse.fq.gz libraryB_forward.fq.gz libraryB_reverse.fq.gz

[kmnip]

@sjackman That script was meant to be a very quick test to see if ABySS could be run from the PATH, but I can probably change it in the next release.

[winni2k]

Cheers!

On Mon, Jan 21, 2019, 7:17 PM Shaun Jackman <notifications@github.com wrote:

Closed #15 https://github.com/bcgsc/transabyss/issues/15.

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