Preprocess#
Data Preprocessing#
We have several functions that are part of our pipeline for processing sequencing data from single-cell lineage tracing technologies:
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Align reads to the TargetSite reference. |
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Call indels from CIGAR strings. |
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Assigns cells to their clonal populations. |
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Collapses close UMIs together from a bam file. |
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Converts FASTQs into an unmapped BAM based on a chemistry. |
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Error-correct cell barcodes in the input BAM. |
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Corrects all intBCs to the provided whitelist. |
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Within cellBC-intBC pairs, collapses UMIs that have close sequences. |
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Filter reads in a BAM that have low quality barcode or UMIs. |
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Filters and corrects a molecule table of cellBC-UMI pairs. |
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Filter out cell barcodes that have too few UMIs or too few reads/UMI. |
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Filters out UMIs with too few reads. |
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Resolve a consensus sequence for each UMI. |
Data Utilities#
We also have several functions that are useful for converting between data formats for downstream analyses:
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Computes indel prior probabilities. |
Converts an AlleleTable into a character matrix. |
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Converts an AlleleTable to a lineage profile. |
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Converts a lineage profile to a character matrix. |