filter_low_expression

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berger juliette

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Dec 15, 2023, 7:36:13 AM12/15/23

to trinityrnaseq-users

Hello Brian,

I'd like to reduce the number of transcripts per gene, so I'm using the filter_low_expr_transcripts.pl script. However I don't quite understand how to use the output. The normalized count matrix hasn't changed. how do I use this result? for further analysis?

Thank you,

Juliette

Brian Haas

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Dec 17, 2023, 9:22:59 AM12/17/23

to berger juliette, trinityrnaseq-users

After filtering the Trinity.fasta to generate a new fasta file, you can redo the quantification (in a new working directory so no earlier intermediates are reused).

You can run trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl
on the new filtered Trinity fasta file to generate a new gene-trans-map file if needed for downstream applications.

best,

Brian

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