Obtain a --gene-trans-map file after rnaSPAdes
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11 months ago
UserA • 0

Hello,

I would like to perform a differential gene analysis on a dataset of 120 paird-end files. I obtained a good de novo quality metatranscriptome using rnaSPAdes (83% of the reads aligned exactly 1 time with bowtie2). I would now like to quantify the transcripts by RSEM using Trinity's align_and_estimate_abundance.pl module. When the metatranscriptome is not made with Trinity but another assembler, a --gene-trans-map file must be provided. But I don't know how to obtain this after assembly with rnaSPAdes, I'm having trouble finding this answer on the Internet (I'm a beginner in bioinformatics). Could you explain the steps to follow or the tools to use?

After this I want to group the sample genes counts into a matrix and then use run_DE_analysis.pl and analyze_diff_expr.pl provided by Trinity.

Thxs!

rnaSPAdes Trinity • 1.1k views
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Following GenoMax comment

This is what you have

NODE_217_length_5488_cov_28.472321_g133_i0 # typical rnaSPAdes transcript header

This is what you want in the gene-trans-map file (two column tabular dataset)

g133    NODE_217_length_5488_cov_28.472321_g133_i0 
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Thxs a lot! I will try like this!

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You could try to create one: https://groups.google.com/g/trinityrnaseq-users/c/qPbWnLl4iY0

While this is from an unrelated software the solution here may be worth considering in your case: https://github.com/Trinotate/Trinotate.github.io/issues/63

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I met the same problem, and does not resolve it. It should be noted that the scripts, such as run_DE_analysis.pl and analyze_diff_expr.pl, provided by Trinity do not work for the output generated by rnaSPAdes since the transcript header made by rnaSPAdes cannot be recognized by Trinity software and its scripts.

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