Bascet-TIRP (.tirp.gz)
TIRP (Tabix-indexed read pairs) is a bgzip’ed text file with the following columns, separated by a tab:
- Name of cell
- 1 (start position in tabix format; ignored)
- 1 (end position in tabix format; ignored)
- R1 sequence
- R2 sequence
- R1 quality score
- R2 quality score
- UMI
With the only exception of right after debarcoding, TIRPs are always sorted by the name of the cell. They are then indexed using tabix. This means that you can retrieve a list of cells in a file using the tabix tool, but we advise you to use higher level wrappers in Zorn/Bascet to not get locked to this file format.
An optional read count histogram can be stored as file: xxx.tirp.gz.hist
Bascet-ZIP (.zip)
We use zip files as a means of storing general data. There are the conventions:
- File Y for cell XX are stored as XX/Y
- If a cells has reads, there are stored as XX/r1.fq and XX/r2.fq
- If a cell has contigs, they are stored as XX/contigs.fa
- The file XX/_mapcell.log is the output from the mapcell script
- Overall, files named XX/YY are reserved as special output from future tools. Thus avoid storing files starting with in their name
Bascet-FASTQ (.R1.fq.gz and .R2.fq.gz)
Some tools require FASTQ as input or output. To keep track of the cell origin of reads, the reads have a special naming convention:
“BASCET_” cellID “:” UMI “:” read_number “:” read_index
where * cellID is the name of the cell. As FASTQ only supports some characters, names will be mangled in the future (to be implemented) * UMI is the unique molecular identifier * read_number is just a number, with the same number for R1 and R2. it can be used to track read correspondence if reads are filtered, multimapped etc. * read_index is 1 or 2, for R1 and R2
Reads in Bascet-FASTQ are typically sorted by cellID, read_number and read_index, in this order. This makes it easy to read all reads for one cell without having to scan through the entire file.
Bascet-BAM (.bam)
To keep track of the cellular origin, reads in BAM files typically follow the same naming convention as in Bascet-FASTQ. Thus, running any aligner on a Bascet-FASTQ should result in valid Bascet-BAM.
To support other tools, the reads may also be annotated using tags. If read names are not named according to the FASTQ scheme, i.e, if they do not start with “BASCET_”, tools must instead scan for tags:
- @CB:Z:…. cell_ID
- @UB:Z….. UMI
This is similar to CellRanger annotation (https://www.10xgenomics.com/support/software/cell-ranger/7.2/analysis/outputs/cr-outputs-bam), except Bascet does not have tags for yet-to-be-corrected cell IDs and UMIs.
Bascet-KRAKEN5 (.kraken5)
This is a sparse matrix HDF5 file, aimed to store counts from KRAKEN2. As KRAKEN2 outputs taxonomy IDs (starting from 0), these are used as column indices in this matrix format.
More details to follow
Bascet-HDF5 (.hd5)
This format loosely implements the Anndata count matrix format (https://anndata.readthedocs.io). To accommodate for the needs to store other types of data, these files will likely deviate from the standard in the future. Thus, do not expect to be able to load them with regular anndata-compatible software.
More details to follow