The bioBakery help forum

Kneaddata FASTQ header problem

Version 0.7.5 of kneaddata does not handle FASTQ headers as seamlessly as earlier versions. With paired FASTQ files for which the headers for both read_1.fastq and read_2.fastq are,

'at’SRR7280791.1 1 length=101
'at’SRR7280791.2 2 length=101
'at’SRR7280791.3 3 length=101

where ‘at’ represents the at symbol. ( The forum script interprets the at symbol as a reference to another user. )
kneaddata reports different read counts for paired output files kneaddata_paired_1.fastq and kneaddata_paired_2.fastq. After massaging the headers to,

'at’SRR7280791.1/1
'at’SRR7280791.2/1
'at’SRR7280791.3/1

for read_1.fastq and,

'at’SRR7280791.1/2
'at’SRR7280791.2/2
'at’SRR7280791.3/2

for read_2.fastq, kneaddata reports identical read counts for the paired output files.