Dataset for `test_full`

[LuisHeinzlmeier]

Description of feature

DOI	Dataset	Description
https://doi.org/10.1186/s13059-018-1603-1	link	This dataset would be perfect, but is missing FASTQ or BAM files.
https://doi.org/10.1038/s41467-019-10756-2	link	Study from demuxem. Human dataset of 8 donors: Page not found. Mice dataset of 2 donors with 4 technical replicates each: Raw FastQ available (But only 4x3 FastQs?).
https://doi.org/10.1186/s13059-020-02032-0	link	Could work, but I did not fully understand the multiplexing. But a maximum of 3 (healthy) + 3 (diseased) = 6 donors.
https://doi.org/10.1186/s13059-018-1603-1	link	8 human donors and individual SNPs of donors. They used demuxlet for deconvolution.

In any case, I will have to perform alignment, etc., since the BAM files are not stored in the databases.

[LuisHeinzlmeier]

Decided on the last dataset with 8 donors. Now, I am trying to reproduce the procedure they described in the method section to obtain all the input files for hadge rescue mode.

[LuisHeinzlmeier]

Summary:

• Generated HTO count matrices using CITE-seq-Count on the GSE108313 FASTQ files (SRR8281307_1/2.fastq.gz), specifying cell barcodes in positions 1–16 and UMIs in positions 17–28, with a cell ceiling of 20,000.

• Generated RNA count matrices, a coordinate-sorted BAM file, and cell barcodes using STARsolo on SRR8281306_1/2.fastq, aligning to the GRCh38 reference genome. Cell barcodes (positions 1–16) and UMIs (positions 17–28, 12bp) were extracted in CB_UMI_Simple mode without a whitelist, with cell filtering via EmptyDrops_CR. I then further filtered the BAM file to reduce its size to ~50 GB (e.g., by removing reads without a cell barcode CB)

• Called genetic variants to produce a VCF using FreeBayes in pooled-continuous mode on the filtered-cell BAM, aligned against the GRCh38 primary assembly. Variants were retained with a minimum alternate allele count of 2, minimum alternate fraction of 1%, and minimum coverage of 6×.

Generated Files:

242K Mar 16 09:45 barcodes.tsv
50G Mar 16 09:45 filtered_cells.bam
36M Mar 16 09:45 freebayes.vcf
631K Mar 16 09:44 hto.tar.gz
65M Mar 16 09:44 rna.tar.gz