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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Test dataset for countASAP package: a lightweight easy to use Python package for processing ASAPseq data

ABSTRACT: A recently developed technique, transposase-accessible chromatin with sequencing (ATAC) with select antigen profiling by sequencing (ASAPseq), provides a combination of chromatin accessibility assessments with measurements of cell- surface marker expression levels. While software exists for the characterization of these datasets, there currently exists no tool explicitly designed to reformat ASAP surface marker FASTQ data into a count matrix which can then be used for these downstream analyses. To address this, we created CountASAP, an easy-to-use Python package purposefully designed to transform FASTQ files from ASAP experiments into count matrices compatible with commonly-used downstream bioinformatic analysis packages. CountASAP takes advantage of the independence of the relevant data structures to perform fully parallelized matches of each sequenced read to user-supplied input ASAP oligos and unique cell-identifier sequences.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Budha Chatterjee

PROVIDER: E-MTAB-15786 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Information management central to JCAHO surveys.

Hospital peer review 20001201 12

Hospitals preparing for Joint Commission surveys should pay close attention to improving organizational performance, says Eric Silfen, former chief medical officer at Reston (VA) Hospital Center, who now oversees the hospital's outcomes research division. ...[more]

PMID: 11188107

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