Hi! Both riboseq and RNA reads are quantifed by Salmon for all transcript isoforms in the gtf? Does anybody have an example output directory I could look at? Thanks to the developers and maintainers.

So, there are run specific results and merged outputs:

test/quantification/salmon/SRX11780879
├── aux_info
│   ├── ambig_info.tsv
│   ├── expected_bias.gz
│   ├── fld.gz
│   ├── meta_info.json
│   ├── observed_bias_3p.gz
│   └── observed_bias.gz
├── cmd_info.json
├── libParams
│   └── flenDist.txt
├── logs
│   └── salmon_quant.log
├── quant.genes.sf
└── quant.sf

4 directories, 11 files

and then the merged outputs:

❯ ll test/quantification/salmon
total 6240
-rw-r--r--@ 1 jackt  staff   167K May  7 16:19 salmon.merged.gene_counts_length_scaled.tsv
-rw-r--r--@ 1 jackt  staff   171K May  7 16:19 salmon.merged.gene_counts_scaled.tsv
-rw-r--r--@ 1 jackt  staff    86K May  7 16:19 salmon.merged.gene_counts.tsv
-rw-r--r--@ 1 jackt  staff   258K May  7 16:19 salmon.merged.gene_lengths.tsv
-rw-r--r--@ 1 jackt  staff   124K May  7 16:19 salmon.merged.gene_tpm.tsv
-rw-r--r--@ 1 jackt  staff   2.1K May  7 16:21 salmon.merged.gene.length_scaled.R_sessionInfo.log
-rw-r--r--@ 1 jackt  staff   165K May  7 16:21 salmon.merged.gene.length_scaled.SummarizedExperiment.rds
-rw-r--r--@ 1 jackt  staff   2.1K May  7 16:21 salmon.merged.gene.R_sessionInfo.log
-rw-r--r--@ 1 jackt  staff   2.1K May  7 16:21 salmon.merged.gene.scaled.R_sessionInfo.log
-rw-r--r--@ 1 jackt  staff   165K May  7 16:21 salmon.merged.gene.scaled.SummarizedExperiment.rds
-rw-r--r--@ 1 jackt  staff   131K May  7 16:21 salmon.merged.gene.SummarizedExperiment.rds
-rw-r--r--@ 1 jackt  staff   387K May  7 16:19 salmon.merged.transcript_counts.tsv
-rw-r--r--@ 1 jackt  staff   650K May  7 16:19 salmon.merged.transcript_lengths.tsv
-rw-r--r--@ 1 jackt  staff   452K May  7 16:19 salmon.merged.transcript_tpm.tsv
-rw-r--r--@ 1 jackt  staff   2.1K May  7 16:21 salmon.merged.transcript.R_sessionInfo.log
-rw-r--r--@ 1 jackt  staff   324K May  7 16:21 salmon.merged.transcript.SummarizedExperiment.rds