single isoform genes are excluded

I get that LIQA was designed for differential isoform abundance analysis, but is there an actual technical reason single isoform genes are excluded from quantification? As is, it would be really nice feature to have for people who want to both do a DE analysis AND an isoform level analysis.

Thank you for you interests in using LIQA and valuable suggestions! Currently we are working on DE detection part and single isoform gene expression will be quantified. Thanks!

Hi~ I just gave LIAQ a try recently. As @nhartwic mentioned, gene names with only one isoform were not found in the .refgene file, and thus, will not be included in the quantification output.
Additionally, since LIQA group genes by gene_names, it is possible that there are two genes with the same gene_name but different gene_ids, e.g. there is such an issue in GENCODE v31. Therefore, using gene_name as the ID will group gene with different gene_ids in terms of their expression levels.

@alanlamsiu Thank you for your feedback. I am updating the code to output single isoform gene read count and expression level.

Is the code updated for this issue?

Should there be any downstream issues if these lines were changed?

LIQA/liqa_src/PreProcess_gtf.pl

Line 133 in 8e09856

if($size >1) ### you can specify the number of the isoform per gene here

LIQA/liqa_src/PreProcess.pl

Line 81 in 8e09856

if($size >1) ### you can specify the number of the isoform per gene here

Should there be any downstream issues if these lines were changed?

LIQA/liqa_src/PreProcess_gtf.pl

Line 133 in 8e09856

if($size >1) ### you can specify the number of the isoform per gene here

LIQA/liqa_src/PreProcess.pl

Line 81 in 8e09856

if($size >1) ### you can specify the number of the isoform per gene here

Hi Thanks! As long as single isoform is included in refgene file, it wont affect downstream analysis. Thanks!

But will it produce stats for these single isoform genes? I want to use LIQA but I want to get counts for single isoform genes as well

Yes, it will produce stats for single isoform genes when you specify size to 0 instead of 1. Thanks!

@huyustats I created a PR (#29) with minimum isoforms per gene added as a command line parameter. I tested it and when set to 2 it produces same results as before (expected behaviour). Do mind checking it?

@huyustats I created a PR (#29) with minimum isoforms per gene added as a command line parameter. I tested it and when set to 2 it produces same results as before (expected behaviour). Do mind checking it?

Thank you! I will check it.