on joined paired end reads
fastq_paired_end_splitter.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$output1_file' '$output2_file'
**What it does**
Splits a single fastq dataset representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have **the same** length.
Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively.
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**Input format**
A multiple-fastq file, for example::
@HWI-EAS91_1_30788AAXX:7:21:1542:1758
GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
+HWI-EAS91_1_30788AAXX:7:21:1542:1758
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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**Outputs**
Left-hand Read::
@HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
+HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
Right-hand Read::
@HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
+HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR