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caleblareau / mgatk

mgatk: mitochondrial genome analysis toolkit
http://caleblareau.github.io/mgatk
MIT License
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BioRad scATAC-seq data #43

Closed liaojinyue closed 2 years ago

liaojinyue commented 2 years ago

Hi, I have sets of scATAC-seq data generated with BioRad platform, which have around 3% total reads mapped to mtDNA. I tried to run mgatk with --barcode-tag changed to "DB" and run into error. Do I need to also change other things in order to run the pipeline? Thanks.

Jason

mgatk tenx -i deconvoluted_data/final/alignments.possorted.tagged.bap.bam  -n mito_test1 -o mito_mgatk -c 5 -bt DB -b count_matrix/barcodes_out.csv -g genomes/mm10/fasta/chrM.fa
Tue Nov 02 12:06:30 HKT 2021: mgatk v0.6.4
Tue Nov 02 12:06:30 HKT 2021: Found bam file: deconvoluted_data/final/alignments.possorted.tagged.bap.bam for genotyping.
Tue Nov 02 12:06:30 HKT 2021: Found file of barcodes to be parsed: count_matrix/barcodes_out.csv
Tue Nov 02 12:06:30 HKT 2021: User specified mitochondrial genome matches .bam file
Tue Nov 02 12:06:30 HKT 2021: Finished determining/splitting barcodes for genotyping.
Tue Nov 02 12:06:30 HKT 2021: Genotyping samples with 5 threads
Error in .subset2(x, i, exact = exact) : subscript out of bounds
Calls: importMito ... importMito.explicit -> levels -> [[ -> [[.data.frame -> <Anonymous>
Execution halted
caleblareau commented 2 years ago

So the short answer is that the DB barcodes are not only ACGT#s, so this throws an error in the Picard function that is the workhorse here. I’ve asked for a modification to Picard a couple of years back, which unfortunately didn’t go through. You will have to run it through bcall, which will work fine, but just be a bit more slow

On Nov 1, 2021, at 9:14 PM, JLiao @.***> wrote:



Hi, I have sets of scATAC-seq data generated with BioRad platform. I tried to run mgatk with --barcode-tag changed to "DB" and run into error. Do I need to also change other things in order to run the pipeline? Thanks.

Jason

mgatk tenx -i deconvoluted_data/final/alignments.possorted.tagged.bap.bam -n mito_test1 -o mito_mgatk -c 5 -bt DB -b count_matrix/barcodes_out.csv -g genomes/mm10/fasta/chrM.fa Tue Nov 02 12:06:30 HKT 2021: mgatk v0.6.4 Tue Nov 02 12:06:30 HKT 2021: Found bam file: deconvoluted_data/final/alignments.possorted.tagged.bap.bam for genotyping. Tue Nov 02 12:06:30 HKT 2021: Found file of barcodes to be parsed: count_matrix/barcodes_out.csv Tue Nov 02 12:06:30 HKT 2021: User specified mitochondrial genome matches .bam file Tue Nov 02 12:06:30 HKT 2021: Finished determining/splitting barcodes for genotyping. Tue Nov 02 12:06:30 HKT 2021: Genotyping samples with 5 threads Error in .subset2(x, i, exact = exact) : subscript out of bounds Calls: importMito ... importMito.explicit -> levels -> [[ -> [[.data.frame -> Execution halted

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