[mikhmv]

solution

The help is here:
read #1 (HWI-ST993:228:C0RWJACXX:6:2316:17166:97507) does not have a matching mate in the same order (HWI-ST993:228:C0RWJACXX:6:2316:12084:97378 found instead)

The Red text should be the same for the same position for reads from Forward and Reverse file. If you manually removed one read from one file you need to remove a read with same file name from the second file

Numbers mean the coordinate on illumina slide. Basically you are trying to put in pairs reads with different coordinates.

[bob-loblaw]

The help is here:
read #1 (HWI-ST993:228:C0RWJACXX:6:2316:17166:97507) does not have a matching mate in the same order (HWI-ST993:228:C0RWJACXX:6:2316:12084:97378 found instead)

The Red text should be the same for the same position for reads from Forward and Reverse file. If you manually removed one read from one file you need to remove a read with same file name from the second file

Numbers mean the coordinate on illumina slide. Basically you are trying to put in pairs reads with different coordinates.

I already tried removing reads from both files, but I got the same problem with a different read. So basically the reads need to be in the same order in each file then? Is there a way to sort a fastq file based on the coordinates?