I am getting the following error when running "Align reads and estimate abundance".
Please help.
Kamran Azim
Error detected: Error, cmd: /usr/local/opt/trinity-2.15.1/util/support_scripts/salmon_trans_to_gene_results.pl output/quant.sf /data/jwd06/main/000/115/273/115273684/working/gene_to_trans.map > output/quant.sf.genes died with ret: 6400 at /usr/local/bin/align_and_estimate_abundance.pl line 729.
Error, encountered 1 failed salmon jobs. See errors above at /usr/local/bin/align_and_estimate_abundance.pl line 905.
Yes, tools within the Trinity suite can be unpredictable and are generally best avoided, or at least at UseGalaxy.org! More details are at trinity.
Instead, for the assembly phase with RNA-seq data, we recommend using rnaSPADes.
Then, for quantification and optionally differential expression, when an assembly is required, we will usually recommend using Salmon.
Run this tool once per sample: Salmon quant Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads
Then input the TMP counts to DESeq2.
Note: be sure to run Salmon with a gene-to-transcript mapping file if the goal is to proceed to DESeq2. You’ll be using the same reference mapping file at both steps: with Salmon, and then later with DESeq2.
Variations may include using Sailfish and/or Kallisto. See the tool forms for usage help and links to author resources/publications. This forum also has some short usage help with a troubleshooting focus when running the tools inside Galaxy workflows.
The final common variation is to not actually fully assemble the reads into a transcriptome, but to generate a psudo-assembly for read abundance counting instead! We have comprehensive walkthroughs of example protocols in our GTN training tutorials, and several IWC production workflows! Which to adapt depends on the data you have available, how finished the underlying genome assembly/annotation is, the species in some cases, and the questions you want to ask.
GTN training tutorials, and several 
IWC production workflows! Which to adapt depends on the data you have available, how finished the underlying genome assembly/annotation is, the species in some cases, and the questions you want to ask.