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README.md

README.md

The BUS format specification

The BUS format is a binary format for storing intermediate results for single cell RNA-Seq datasets. This repository details the specification of the format.

The motivation and example usage of the BUS format is described in

P Melsted, V Ntranos, L Pachter, The Barcode, UMI, Set format and BUStools, Bioinformatics, btz279, 2019.

Tools

BUS generation

BUS file manipulation

BUS parsing

Format specification

A BUS file is a binary file consisting of a header followed by zero or more BUS records. Each BUS header consists of the following elements in order

Field name Description Type Value
magic fixed magic string char[4] BUS\0
version BUS format version uint32_t
bc_len Barcode length [1-32] uint32_t
umi_len UMI length [1-32] uint32_t
tlen Length of plain text header uint32_t
text Plain text header char[tlen]

The encoding used for the text header is ASCII.

BUS records are stored directly after the header in the following format, the size of each BUS record is rounded up to 32 bytes. This is done by adding 32 unused bits at the end of the record.

Field name Description Type
barcode 2-bit encoded barcode uint64_t
umi 2-bit encoded UMI uint64_t
ec equivalence class int32_t
count fragment count uint32_t
flags flags uint32_t

The flags column can be used to store extra information, but the format specification of BUS files does not put any restrictions or specify the content.

The 2-bit encoding encodes A,C,G,T and 00,01,10,11, and such that the first nucleotides are encoded in the most significant bits. For example the barcode GCCA corresponds to the bit code 10010100 or the integer 148. All integers are encoded as little-endian.

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