[mira_talk] Re: Doubt about read groups to do a denovo transcriptome assembly
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 3 Feb 2014 14:25:43 +0000
On Mon, Feb 3, 2014 at 2:09 PM, Camila M. <kamynz16@xxxxxxxxx> wrote:
> Hi all,
>
> I'm trying to do a denovo transcriptome assembly, and I have been doing a
> small test with a small proportion of my data. I used Illumina, but I have
> several doubts, after I read the MIRA manual.
>
> First, I have a paired-end library, and I'm not sure how to specify from the
> sequences from the R1 reads and the R2 reads. Do I have to separate the
> sequences for read groups
>
> Here is an example of my manifest file:
>
> project = 1_test
> job = est,denovo,accurate
> parameters = -GE:not=1 -NW:cmrnl=no
>
> readgroup = Test_R1
> data =
> /host/Users/CamilaMV/Desktop/DOCUMENTOS_LINUX_MINT/BRAZIL/Script_cluster/FROM_CLUSTER/files_to_MIRA/R1.fastq
> technology = solexa
> strain = pseudozyma
> segment_placement = ---> <---
>
> readgroup = Test_R2
> data =
> /host/Users/CamilaMV/Desktop/DOCUMENTOS_LINUX_MINT/BRAZIL/Script_cluster/FROM_CLUSTER/files_to_MIRA/R2.fastq
> technology = solexa
> strain = pseudozyma
> segment_placement = ---> <---
>
>
> Thanks in advance,
The naming R1 and R2 normally means paired reads from the read group.
Try a single readgroup using both files.
Peter
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