seqfu deinterleave
deinterleave (or dei) is one of the core subprograms of SeqFu. It's used to produce two separate FASTQ files from an interleaved file.
ilv: interleave FASTQ files
Usage: dei [options] -o basename <interleaved-fastq>
-o --output-basename "str" save output to output_R1.fq and output_R2.fq
-f --for-ext "R1" extension for R1 file [default: _R1.fq]
-r --rev-ext "R2" extension for R2 file [default: _R2.fq]
-c --check enable careful mode (check sequence names and numbers)
-v --verbose print verbose output
-s --strip-comments skip comments
-p --prefix "string" rename sequences (append a progressive number)
notes:
use "-" as input filename to read from STDIN
example:
dei -o newfile file.fq
Streaming
If a program produce an interleaved output, seqfu deinterleave can be used in a pipe (specifying "-" as input):
fu-primers -1 file_R1.fq -2 file_R2.fq | seqfu deinterleave -o fileNoPrimers -
What are interleaved files?
Paired end sequences can be stored in two separate files (usually denoted with the _R1 and _R2 strings) or in a single sequence where each sequence pair is stored as two subsequent sequences.
A simple example is depicted below:
=======================================================================
File_R1.fq File_R2.fq Interleaved.fq
=======================================================================
@seq1 @seq1 @seq1
TTTCATTCTGACTGCAACG GGATTAAAAAAAGAGTGTC TTTCATTCTGACTGCAACG
+ + +
IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII
@seq2 @seq2 @seq1
GTGTGGATTAAAAAAAAAA TTTTTTTTTTTTTTTTTTT GGATTAAAAAAAGAGTGTC
+ + +
IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII
@seq3 @seq3 @seq2
AGAGTGTCTGATAGCA GATAGCAG GTGTGGATTAAAAAAAAAA
+ + +
IIIIIIIIIIIIIIII IIIIIIII IIIIIIIIIIIIIIIIIII
@seq2
TTTTTTTTTTTTTTTTTTT
+
IIIIIIIIIIIIIIIIIII
@seq3
AGAGTGTCTGATAGCA
+
IIIIIIIIIIIIIIII
@seq3
GATAGCAG
+
IIIIIIII
Screenshot
