gene_trans_map

[Ryan]

Hi,

Is there some sort of function that can generate the equivalent of a trinity gene_trans_map from trans-abyss transcriptome assemblies?

Thanks!

[Ka Ming Nip]

Hi,

I presume you are trying to get the counts.

If you run RSEM directly, then you can use the option `--transcript-to-gene-map <file>` for its script `rsem-prepare-reference` as explained here:

http://deweylab.biostat.wisc.edu/rsem/rsem-prepare-reference.html

Hope that helps!

Ka Ming

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

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From: trans...@googlegroups.com <trans...@googlegroups.com> on behalf of Ryan <ryan.g...@gmail.com>
Sent: September 11, 2018 11:31 PM
To: Trans-ABySS
Subject: gene_trans_map

 

Hi,

Is there some sort of function that can generate the equivalent of a trinity gene_trans_map from trans-abyss transcriptome assemblies?

Thanks!

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[Ryan]

Thanks for your help, Ka Ming.

I'm not sure that this does exactly what I want. I have a non-model organism and lack a quality genome with known gene coordinates. It seems that the --transcript-to-gene-map <file> option assumes that I already have a transcript to gene map, but what I'd like to do is generate that file. Or am I misunderstanding something?

Best,

Ryan

[Ka Ming Nip]

Hi Ryan,

I don't think you misunderstood anything here. :)

Do you have the genomic sequencing reads of your organism?

You can generate a spliced graph using a transcriptome assembly and the corresponding genomic reads using our tool called ChopStitch:

https://github.com/bcgsc/ChopStitch

Once you have the splice graph, you can treat each subgraph as a "gene".

Hope that helps!

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 Ryan <ryan.g...@gmail.com>

Sent: September 12, 2018 11:31 PM
To: Trans-ABySS
Subject: Re: gene_trans_map