Delaney Sullivan

Can't really tell unless I see the commands used and how the index was generated.

Thanks for bringing up this issue; it seems to be specific for the lamanno workflow (which we're deprecating in favor of something better). The way you're running the programs is...

I've identified the issue: it's because the lamanno workflow is poorly implemented. Every single intron is considered a unique "transcript". You have k-mers in the index that can potentially map...

1. Correct 2. Yes 3. Likely (however, I haven't tested it out with the lamanno workflow). If you use our upgraded workflow (--workflow=nac), you'll get much lower memory usage (for...

Can you show the commands you’re using and how you’re building the index (what FASTA/GTF files are being used) as well as the commands you’re using for kb count? kb...

Can you run /usr/bin/time -v (include the -v) And then use --verbose when using kb count? It works on my end. Edit: It takes 18 gb on my end for...

It says "Maximum resident set size (kbytes): 548888" That is only 0.5 gigabytes. The "Signals.SIGILL: 4" means illegal instruction. That likely means that the prepackaged binaries do NOT work on...

kallisto is an RNAseq quantification algorithm that assesses gene expression -- if you have two reads originating from the same transcript, that transcript will get two counts. That's how gene...

I don’t really think there is a way to check for that. FASTQ files are just DNA base sequences, and there’s no way for a program to know what file...

That would be possible — I often work with FASTQs with altered read names, but perhaps a warning could be printed out if the names don’t match. Will consider it.