[mira_talk] Doubt about read groups to do a denovo transcriptome assembly
- From: "Camila M." <kamynz16@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 3 Feb 2014 09:09:29 -0500
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,
--
Camila M.
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