• Trinity: Frequently Asked Questions
• There are too many transcripts! What do I do?
• What computing resources are required?
• How long should this take?
• How do I use reads I downloaded from SRA?
• Other example strategies for downloading directly from SRA via fastq-dump:
• How can I run this in parallel on a computing grid?
• How do I identify the specific reads that were incorporated into the transcript assemblies?
• How do I combine paired-end and single-end reads?
• How do I combine strand-specific and non-strand-specific reads?
• Trinity process died due to 'std::bad_alloc'
• Butterfly fails with java Error: Cannot create GC thread. Out of system resources.
• Last resort - sharing your data privately with Trinity developers for debugging