James Boot

For building kallisto index I'm using the Ensembl Homo_sapiens.GRCh38.cdna.all.fa , below is the command: kallisto index -i /path/to/index /path/to/Homo_sapiens.GRCh38.cdna.all.fa.gz Running psuedo-alignment: kallisto quant -i /path/to/index/ \ -o $SUBDIR \ -b...

That makes sense, thanks for your help. Is there are cDNA FASTA file you would recommend using?

Hi Patrick, Thanks very much for your quick response. I tried running without the whitelist (all other options the same as above) but still got the same error message: ```...

Sorry for taking some time to come back to this. Running with pandas 1.4 fixed the problem for me too! Thanks for your help!

Hi, to add to this, we recently used the kraken2 PlusPFP-16 reference downloaded from: https://benlangmead.github.io/aws-indexes/k2 - we ran kraken with default parameters and found no reads classified to plant genomes....

I get the same error using the following code: ``` annots = c('hg38_cpgs', 'hg38_basicgenes') annotations = build_annotations(genome = 'hg38', annotations = annots) ``` Any help greatly appreciated!