fasta output headers

[fre...@uci.edu]

I noticed that in the headers for the output .cds and .pep files that the fasta headers don't include the gene IDs from the input gtf/fasta file, and I was wondering if this is on purpose, especially considering that the transcript ID is duplicated 3 times in the same fasta header. It seems unnecessary and would be useful to have the gene IDs in the fasta headers as well. I've written a script to solve this but the more I think about it the more I imagine that the gene IDs were supposed to make it into the fasta output. I've attached a picture of the output .pep file from a run with the headers underlined.

[Brian Haas]

Hi,

If you provide the --gene_trans_map file to the TransDecoder.LongOrfs step, it should use that to retain any original gene/transcript relationship info and carry it through.  You'd need to rerun from the beginning in a clean workspace, though, since it would otherwise try to reuse earlier generated outputs, in the case you want to give it a whirl.

best,

~b

On Wed, Jan 16, 2019 at 1:51 PM <fre...@uci.edu> wrote:

I noticed that in the headers for the output .cds and .pep files that the fasta headers don't include the gene IDs from the input gtf/fasta file, and I was wondering if this is on purpose, especially considering that the transcript ID is duplicated 3 times in the same fasta header. It seems unnecessary and would be useful to have the gene IDs in the fasta headers as well. I've written a script to solve this but the more I think about it the more I imagine that the gene IDs were supposed to make it into the fasta output. I've attached a picture of the output .pep file from a run with the headers underlined.

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Brian J. Haas
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[fre...@uci.edu]

Thanks!