[scAPP] record qc metrics from 10x pipeline's output - Githubissues

epigen-UCSD / epigen_ucsd_django

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[scAPP] record qc metrics from 10x pipeline's output #419

Open biomystery opened 4 years ago

biomystery commented 4 years ago

should be the metrics in summary.csv

10xATAC outputs/10xATAC/MM_125/outs/summary.csv
10xRNA: wait for a example

think about ways to

store these metrics: can create a table with those columns inside the summary.csv (do 10xATAC first)
display these metrics: data.table or other means?

biomystery commented 4 years ago

[ ] need a example for sc/snRNA-seq
[ ] thinking about inheritance class [a general class for single-cell-qc, then expanded to different experiments (internal classes)
[ ] externally decide a way to display the content (write method for that)
[ ] UI/GUI which place to put

biomystery commented 4 years ago

what to show: RNA:

id | estimated_number_of_cells | mean_reads_per_cell | median_genes_per_cell | number_of_reads | valid_barcodes | sequencing_saturation | q30_bases_in_barcode | q30_bases_in_rna_read | q30_bases_in_sample_index | q30_bases_in_UMI | reads_mapped_to_genome | reads_mapped_confidently_to_genome | reads_mapped_confidently_to_intergenic_regions | reads_mapped_confidently_to_intronic_regions | reads_mapped_confidently_to_exonic_regions | reads_mapped_confidently_to_transcriptome | reads_mapped_antisense_to_gene | frac_reads_in_cells | total_genes_detected | median_UMI_counts_per_cell

ATAC:

id | annotated_cells | bc_q30_bases_fract | cellranger_atac_version | cells_detected | frac_cut_fragments_in_peaks | frac_fragments_nfr | frac_fragments_nfr_or_nuc | frac_fragments_nuc | frac_fragments_overlapping_peaks | frac_fragments_overlapping_targets | frac_mapped_confidently | frac_waste_chimeric | frac_waste_duplicate | frac_waste_lowmapq | frac_waste_mitochondrial | frac_waste_no_barcode | frac_waste_non_cell_barcode | frac_wast e_overall_nondup | frac_waste_total | frac_waste_unmapped | median_fragments_per_cell | num_fragments | r1_q30_bases_fract | r2_q30_bases_fract | si_q30_bases_fract | total_usable_fragments | tss_enrichment_score

biomystery commented 4 years ago

RNA: estimated_number_of_cells| mean_reads_per_cell| median_genes_per_cell |sequencing_saturation| median_UMI_counts_per_cell|frac_reads_in_cells

ATAC: annotated_cells vs cells_detected (pick one)

annotated_cells| tss_enrichment_score| median_fragments_per_cell | frac_fragments_overlapping_peaks|percent duplicates

percent duplicates =frac_waste_duplicate = sequencing_saturation (in RNA)

biomystery commented 4 years ago

select and export: https://docs.google.com/spreadsheets/d/1AuIQg327zigoo8byycSaa1LZkUd_kok1g05Kq3lJi7Y/edit?usp=sharing