jefftc
commented
1 year ago Hi Joao,
To do this, you will need to skip the early part of the pipeline where it deconvolutes the CellRanger results and provide from your SmartSeq data one BAM for each cell.
If you look in the Snakefile, the output files created in each step of the workflow are documented. We would be skipping step 02_demux, and starting with the files in step 03_preproc.
One complication is that the pipeline processes batches of cells together so that it runs faster. However, since you are using SmartSeq, you won't be working with as many cells as 10X, so it will not be computationally prohibitive to run all the cells into one batch. You can simplify the pipeline for yourself by just processing all the cells for each sample in a single batch. To do this, set in the Snakefile, the following parameter to a very large number (larger than the total number of cells): CELLS_PER_BATCH_PREPROCESSING = 999999
Then, try starting with: data/ cells.txt genome.fa known_sites1.vcf.gz known_sites1.vcf.gz.tbi known_sites2.vcf.gz known_sites2.vcf.gz.tbi known_sites3.vcf.gz known_sites3.vcf.gz.tbi output/ 03_preproc/{sample}.0.cells.bam/ {cell}.bam
The data/ directory is set up the same way, except no cell ranger results are needed.
The output/03_preproc/{sample}.0.cells.bam/ directory (for {sample} and batch 0, the only batch) contains the BAM files for each cell from {sample}. The BAM files should be named {cell}.bam where {cell} is the name of the cell (it can be a barcode, or the plate location, etc).
I haven't tested this, and it's possible there's some header information in the BAM files that may need to be fixed. In any case, please run this and let me know if you run into problems.
Thanks, Jeff
On Aug 30, 2023, at 5:18 AM, Joao MF Alves @.***> wrote:
Hi, Thanks for this very useful package! I'm interesting in running the tool on some smart-seq2 datasets. How should I set up the files so that I can keep using the same snakefile? Thanks in advance, Joao — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>
jmfa
Hi, Thanks for this very useful package! I'm interesting in running the tool on some smart-seq2 datasets. How should I set up the files so that I can keep using the same snakefile?
Thanks in advance, Joao