Delaney Sullivan
Delaney Sullivan
Hmm, maybe R2 then R1? How about looking at a few reads manually and running them through NCBI BLAST?
1. No 2. Nothing 3. I think so? But very easy to check once you get the pseudoalignments working. It will be very obvious if something’s off (I.e. no barcodes...
Are you using "kb count"? Try specifying --num instead of -n.
A couple of suggestions: 1. Make sure you're using the index built with the kallisto 0.50.1 with the kallisto 0.50.1 quant (don't use an index build with an older kallistio...
Thank you so much! I have been looking into these issues related to these instruction sets. I think we should add an option to disable it directly when 'cmaking' kallisto...
We do have a --genomebam in the devel version of kb that's fully functional (and it will be added into the next stable release of kb). See https://github.com/pachterlab/kb_python/pull/184
BD Rhapsody is single-end (paired-end doesn't mean you have an R1 and R2, it means you have two sequences on a fragment that are sequenced together).
Everything is technically supported by kallisto if you specify the proper technology string and the list of barcodes. It’s not built in directly in kallisto, but you can customize the...
You're indexing the genome, not the transcriptome. Kallisto requires you to index the transcriptome. Homo_sapiens.GRCh38.dna.primary_assembly.fa is a genome FASTA file, not a transcriptome FASTA file.
You need to compile with -DUSE_BAM=ON in cmake. I haven’t throughly tested whether BAM works though, so FASTQ is the safer option in terms of avoiding bugs. Your other commands...