Closed hchintalapudi closed 3 years ago
Here you're checking for every possible barcode, since you did not do any filtering of the metadata table. In the merge vignette, we apply an initial count-based cutoff to retain a set of cell barcodes for later analysis. Since you include all barcodes here, many will be present at extremely low frequency in the fragment file, and so most are not able to be detected in the fragment file checks that we perform.
Right, I skipped that step as I intuitively did not know which field to use for filtering, as 'passed_filters' is not present in my metadata file. That's because I have multiome data and the format/fields are little different.
From my old scATAC data:
colnames(singlecell)
[1] "duplicate" "chimeric" "unmapped"
[4] "lowmapq" "mitochondrial" "passed_filters"
[7] "cell_id" "is__cell_barcode" "TSS_fragments"
[10] "DNase_sensitive_region_fragments" "enhancer_region_fragments" "promoter_region_fragments"
[13] "on_target_fragments" "blacklist_region_fragments" "peak_region_fragments"
[16] "peak_region_cutsites"
Current MULTIome data:
colnames(md.zmel_c)
[1] "gex_barcode" "atac_barcode" "is_cell"
[4] "excluded_reason" "gex_raw_reads" "gex_mapped_reads"
[7] "gex_conf_intergenic_reads" "gex_conf_exonic_reads" "gex_conf_intronic_reads"
[10] "gex_conf_exonic_unique_reads" "gex_conf_exonic_antisense_reads" "gex_conf_exonic_dup_reads"
[13] "gex_exonic_umis" "gex_conf_intronic_unique_reads" "gex_conf_intronic_antisense_reads"
[16] "gex_conf_intronic_dup_reads" "gex_intronic_umis" "gex_conf_txomic_unique_reads"
[19] "gex_umis_count" "gex_genes_count" "atac_raw_reads"
[22] "atac_unmapped_reads" "atac_lowmapq" "atac_dup_reads"
[25] "atac_chimeric_reads" "atac_mitochondrial_reads" "atac_fragments"
[28] "atac_TSS_fragments" "atac_peak_region_fragments" "atac_peak_region_cutsites"
What's the best way to filter based on the metadata I have? Probably with "excluded_reason"? from CellRanger Thanks for your help.
Explanation of the cellranger ARC metadata outputs is here: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/per_barcode_metrics
"atac_fragments" would be the total counts per barcode
Aah! Thank you.
Hello, I was following the merge vignette and I get an error when I try to create a fragment object.
Here is my code:
My unzipped fragment file:
I see in #748 that you mention 5 columns being present in the fragment file and it looks like I have 5 columns. What could've gone wrong in my case?
Thank you.