Caleb Lareau
Caleb Lareau
thanks for the note! we definitely had some tunnel vision when writing this. your edits make perfect sense to me and I will try to update the package in the...
added in 0.7.1
Sure! For preprocessing fastqs: ``` python3 asap_to_kite/asap_to_kite_v2.py -f intracellular_fastqs -s ICA_CKDL240020949-1A -c 12 -o ICA ``` then ``` kallisto bus -i feature_reference.idx -x 10xv2 -t 12 -o ICA ICA_R1.fastq.gz ICA_R2.fastq.gz...
Everything else is there, so its an issue with the R installation. Can you verify your `R` executable version has these packages: - GenomicRanges - data.table - SummarizedExperiment - Matrix
The issue is the fasta you supply to mgatk should only be the mito genome (or use one of the built in ones). On Aug 16, 2024, at 9:20 AM,...
The bam file can have more than just the mitochondrial chromosome contig. The issue is probably that the text following the > should match exactly the chromosome name (e.g., `>chrM`)....
echoing ``` pip3 install --force-reinstall -v "pulp==2.7" ``` as very useful talking to another user, there was an error with java that wasn't obvious which can be discovered via ```...