All paired-end read unmatched

[cfeb]

@Eric_Vallender

It seems like an error in the coding of the “-strict” flag (which is also the default). Adding the " --decontaminate-pairs=lenient" will largely fix the problem (though you now will have that particular effect on your results).

Hi, this solution works for me while changing the sequence labels does not. Can anyone direct me to the documentation that shows the difference between applying this “–decontaminate-pairs=lenient” option compared to the standard output?

[sagunmaharjann]

Hi all,

Thank you for reaching out to the bioBakery Lab forum.

Form Kneaddata>=v0.11.0, there is an option for --input1 and --input2 so if the read identifiers are the same in both pairs, no modification to the input files are necessary as Kneaddata will automatically take care of it.

Regards,
Sagun

[fquerdasi]

Hello,

I am using kneaddata v0.12.0 with the options --input1 and --input2 specified, and have encountered the same issue others have described. My sequence identifiers are @A00674:488:HGYKGDSX5:1:1101:3965:1000 1:N:0:ACGATCAG+GAGACGAT for R1, and @A00674:488:HGYKGDSX5:1:1101:3965:1000 2:N:0:ACGATCAG+GAGACGAT for R2.

In other words, the read identifiers appear to be the same in both pairs.
I used default parameters for bowtie2.