fastx_barcode_splitter.pl - Online in the Cloud

PROGRAM:

NAME

fastx_barcode_splitter.pl - FASTX Barcode Splitter

DESCRIPTION

Barcode Splitter, by Assaf Gordon (gordon@cshl.edu), 11sep2008

This program reads FASTA/FASTQ file and splits it into several smaller files, Based on
barcode matching. FASTA/FASTQ data is read from STDIN (format is auto-detected.) Output
files will be writen to disk. Summary will be printed to STDOUT.

usage: r.pl --bcfile FILE --prefix PREFIX [--suffix SUFFIX] [--bol|--eol]

[--mismatches N] [--exact] [--partial N] [--help] [--quiet] [--debug]

Arguments:

--bcfile FILE - Barcodes file name. (see explanation below.) --prefix PREFIX - File
prefix. will be added to the output files. Can be used

to specify output directories.

--suffix SUFFIX - File suffix (optional). Can be used to specify file

extensions.

--bol - Try to match barcodes at the BEGINNING of sequences.

(What biologists would call the 5' end, and programmers would call index 0.)

--eol - Try to match barcodes at the END of sequences.

(What biologists would call the 3' end, and programmers would call the end of the
string.) NOTE: one of --bol, --eol must be specified, but not both.

--mismatches N - Max. number of mismatches allowed. default is 1. --exact - Same
as '--mismatches 0'. If both --exact and --mismatches

are specified, '--exact' takes precedence.

--partial N - Allow partial overlap of barcodes. (see explanation below.)

(Default is not partial matching)

--quiet - Don't print counts and summary at the end of the run.

(Default is to print.)

--debug - Print lots of useless debug information to STDERR. --help -
This helpful help screen.

Example (Assuming 's_2_100.txt' is a FASTQ file, 'mybarcodes.txt' is the barcodes file):

$ cat s_2_100.txt | /build/fastx-toolkit-V6DvdY/fastx-toolkit-0.0.14/debian/fastx-
toolkit/usr/bin/fastx_barcode_splitter.pl --bcfile mybarcodes.txt --bol
--mismatches 2

--prefix /tmp/bla_ --suffix ".txt"

Barcode file format ------------------- Barcode files are simple text files. Each line
should contain an identifier (descriptive name for the barcode), and the barcode itself
(A/C/G/T), separated by a TAB character. Example:

#This line is a comment (starts with a 'number' sign) BC1 GATCT BC2 ATCGT BC3 GTGAT
BC4 TGTCT

For each barcode, a new FASTQ file will be created (with the barcode's identifier as part
of the file name). Sequences matching the barcode will be stored in the appropriate file.

Running the above example (assuming "mybarcodes.txt" contains the above barcodes), will
create the following files:

/tmp/bla_BC1.txt /tmp/bla_BC2.txt /tmp/bla_BC3.txt /tmp/bla_BC4.txt
/tmp/bla_unmatched.txt

The 'unmatched' file will contain all sequences that didn't match any barcode.

Barcode matching ----------------

** Without partial matching:

Count mismatches between the FASTA/Q sequences and the barcodes. The barcode which
matched with the lowest mismatches count (providing the count is small or equal to
'--mismatches N') 'gets' the sequences.

Example (using the above barcodes): Input Sequence:

GATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG

Matching with '--bol --mismatches 1':
GATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG GATCT (1 mismatch, BC1) ATCGT (4 mismatches,
BC2) GTGAT (3 mismatches, BC3) TGTCT (3 mismatches, BC4)

This sequence will be classified as 'BC1' (it has the lowest mismatch count). If
'--exact' or '--mismatches 0' were specified, this sequence would be classified as
'unmatched' (because, although BC1 had the lowest mismatch count, it is above the maximum
allowed mismatches).

Matching with '--eol' (end of line) does the same, but from the other side of the
sequence.

** With partial matching (very similar to indels):

Same as above, with the following addition: barcodes are also checked for partial overlap
(number of allowed non-overlapping bases is '--partial N').

Example: Input sequence is ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG (Same as above, but note
the missing 'G' at the beginning.)

Matching (without partial overlapping) against BC1 yields 4 mismatches:
ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG GATCT (4 mismatches)

Partial overlapping would also try the following match:
-ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG

GATCT (1 mismatch)

Note: scoring counts a missing base as a mismatch, so the final mismatch count is 2 (1
'real' mismatch, 1 'missing base' mismatch). If running with '--mismatches 2' (meaning
allowing upto 2 mismatches) - this seqeunce will be classified as BC1.

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