Extracting Cell Barcodes from scWGBS Protocols

Cell barcodes are commonly used in scRNA-seq protocols to overcome DNA input issues and increase throughput by merging cDNA from separate wells into a single well. In a similar manner, the single-cell WGBS (scWGBS) protocol, snmc-seq2, uses the same methodology for increasing throughput. While most current scWGBS protocols do not use cell barcodes, it is possible (some may say likely) that cell barcodes and unique molecular indexes (UMIs) will be used more frequently in future protocols.

BISCUIT provides the biscuit bc subcommand as a way to remove uncorrected cell barcodes from FASTQ files, which can either be written to new FASTQ files or fed directly into biscuit align. The output from biscuit bc is compatible with umi-tools which allows the user to use umi-tools for barcode correction and then pass the resulting FASTQs as input to biscuit align.

NOTE: It is suggested to not used BISCUIT version 1.3.0 for extracting cell barcodes as it is not compatible with umi-tools and contains minor differences in the SAM entry from later versions of BISCUIT (version 1.3.1-dev onward). Please use at least BISCUIT 1.4.0 when utilizing biscuit bc.

Barcode Extraction with BISCUIT

biscuit bc takes FASTQs as input and outputs the processed reads to standard out:

# Single-end data
biscuit bc read1.fq.gz

# Paired-end data
biscuit bc read1.fq.gz read2.fq.gz

For paired-end data, the output is printed in an interleaved form (i.e., read 1 followed by read 2 for each read pair). It is important to include both FASTQs as input for paired-end data, as the barcode and an artificial UMI (needed for compatibility with umi-tools) are written to the read name of both read 1 and read 2.

You can set the the cell barcode location with the -m/--mate, -s/--bc-start, and -l/--bc-length options.

biscuit bc -m 1 -s 1 -l 8 read1.fq.gz read2.fq.gz

-m/--mate specifies the mate the barcode is in (1 or 2), -s/--bc-start is the start position of the barcode (given as a 1-based number), and l/--bc-length is the length of the barcode.

Rather than writing the processed reads to standard out, you can instead write them to a FASTQ file with -o/--output-prefix, which is the basename of your output FASTQ files. For single-end data, .fq.gz will be appended to your output prefix. Paired-end data will have _R1.fq.gz or _R2.fq.gz appended to the prefix for reads 1 and 2, respectively.

biscuit bc -o my_processed_reads read1.fq.gz read2.fq.gz

For more help on available flags, run biscuit bc in the terminal or visit the bc help page.

Passing Ouput to biscuit align

The output of biscuit bc can be passed straight to biscuit align:

# Single-end data
biscuit bc read1.fq.gz | \
biscuit align -9 -@ NTHREADS /path/to/my_reference.fa -

# Paired-end data
biscuit bc read1.fq.gz read2.fq.gz | \
biscuit align -p -9 -@ NTHREADS /path/to/my_reference.fa -

The -9 flag tells biscuit align to extract barcodes from the read name, while the -p flag for paired-end data is needed to handle the interleaved input from biscuit bc.

You can also align FASTQs that were created by biscuit bc:

# Single-end data
biscuit bc -o reads my_se_data.fq.gz
biscuit align -9 -@ NTHREADS /path/to/my_reference.fa reads.fq.gz

# Paired-end data
biscuit bc -o reads my_pe_data_R1.fq.gz my_pe_data_R2.fq.gz
biscuit align -9 -@ NTHREADS /path/to/my_reference.fa read_R1.fq.gz read_R2.fq.gz

In either case, the cell barcode is placed in the CB SAM tag (“the optionally corrected cellular barcode sequence”), while the UMI is placed in the RX SAM tag (the “[s]equence bases from the unique molecular identifier … [where] the value may be non-unique in the file.”)

Barcode Correction with umi-tools

Barcode correction and extraction can be performed using umi-tools with the help of synthbar (here shown for paired-end sequencing).

Step 1: Add synthetic UMI with synthbar

umi-tools requires reads to have a UMI. At this time, there are no scWGBS protocols that include UMIs; therefore, a synthetic UMI sequence must be added to the read with the cell barcode in it. synthbar is a tool that can add synthetic sequences to cells and, for our purposes, can be used to add a synthetic UMI:

synthbar -b AAAAAAAA barcoded_reads_R1.fastq.gz | \
gzip > barcoded_with_umi_R1.fastq.gz

This will prepend AAAAAAAA to the start of each read in the input FASTQ file, which can be treated as the UMI for each read.

Step 2: Create Whitelist

Using umi-tools requires two steps. The first step is to process your FASTQ with the cell barcodes in it and try to find the most likely true cell barcode:

umi_tools whitelist \
    --log2stderr \
    --bc-pattern=NNNNNNNNCCCCCCC \
    --stdin barcoded_with_umi_R1.fastq.gz \
> whitelist.txt

Here, NNNNNNNNCCCCCCC specifies a an 8 basepair UMI followed by a 7 basepair cell barcode.

Step 3: Correct and Extract Barcodes

The results from whitelist.txt are then fed into the code that extracts the UMI and cell barcode into the read name:

umi_tools extract \
    --bc-pattern=NNNNNNNNCCCCCCC \
    --whitelist=whitelist.txt \
    --error-correct-cell \
    --stdin barcoded_with_umi_R1.fastq.gz \
    --stdout barcoded_with_umi_R1_corrected.fastq.gz \
    --read2-in barcoded_reads_R2.fastq.gz \
    --read2-out barcoded_reads_R2_corrected.fastq.gz

Passing to biscuit align

The resulting FASTQs can then be passed into biscuit align in a similar manner to extracting barcodes with biscuit bc:

biscuit align -9 -@ NTHREADS /path/to/my_reference.fa \
    barcoded_with_umi_R1_corrected.fastq.gz \
    barcoded_reads_R2_corrected.fastq.gz
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