seqfu deinterleave
deinterleave (ordei) is one of the core subprograms ofSeqFu. 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 STDINexample: dei -o newfile file.fqStreaming
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 @seq1TTTCATTCTGACTGCAACG GGATTAAAAAAAGAGTGTC TTTCATTCTGACTGCAACG+ + +IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII@seq2 @seq2 @seq1GTGTGGATTAAAAAAAAAA TTTTTTTTTTTTTTTTTTT GGATTAAAAAAAGAGTGTC+ + +IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII@seq3 @seq3 @seq2 AGAGTGTCTGATAGCA GATAGCAG GTGTGGATTAAAAAAAAAA+ + +IIIIIIIIIIIIIIII IIIIIIII IIIIIIIIIIIIIIIIIII @seq2 TTTTTTTTTTTTTTTTTTT + IIIIIIIIIIIIIIIIIII @seq3 AGAGTGTCTGATAGCA + IIIIIIIIIIIIIIII @seq3 GATAGCAG + IIIIIIIIScreenshot
