I would not use the genome of closely-related species for this. It may add more confusion than benefits, unless that are super closely related.
T.
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I would not use the genome of closely-related species for this. It may add more confusion than benefits, unless that are super closely related.
T.
From: trinityrn...@googlegroups.com [mailto:trinityrn...@googlegroups.com] On Behalf Of Farbod Emami
Sent: August 23, 2016 1:45 PM
To: trinityrnaseq-users <trinityrn...@googlegroups.com>
Subject: [trinityrnaseq-users] How to begin genome-guided Trinity
Hi Dear Trinity experts,
Sorry for this very simple question,
I have used my 3 males and 3 females (12 paired-end fastq files) non-model fish for de-novo assembly using Trinity.
Now, I want to run Genome-guided approach but I do not know how to began to create "read alignments to Trinity as a coordinate-sorted bam file" and "coordinate sorted bam file"
I have find a related species genome from here and I want to use STAR for my other steps.
Do I must align each samples (e.g: first sample1-left.fastq & sample1-right.fastq and then sample2 . . . ) separately to the genome ?
Do I must use "bowtie-build" command first on the Genome file ?
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It is not clear from the figure, but I will assume that when they say draft genome, they mean the Guppy draft genome. That’s fine. It does not have to be a final genome. However, using a closely related species is another story. For one, you assuming most genes are organized in the same way in the genome (unlikely), 2 you are assuming the gene duplications is equal between both genomes (unlikely), you are assuming genes are conserved enough for the genome to actually help you (possible, but unlikely).
Why not just do a de-novo assembly? That’s one of Trinity’s main strengths.
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Hi Farbod,
As you already have a de novo assembly just blast the DEGs against the genome and hopefully they will hit an annotated gene. Although if there was no hit in the first place I think it's unlikely you'll get a lot from searching the genome.
Best, Mark
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Yes that would be my suggestion if the genome isn't in ncbi.
Dear Dr. Mark, Hi.
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Thank you,
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Thank you,
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Dr. Mark A. Chapman------------------------------------Centre for Biological Sciences
University of SouthamptonLife Sciences Building 85
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