I have some Illumina MiSeq data (sequenced beginning 2015). The reads are paired-end 2x250 bp. I need to cut 100 bp of the end of each read. Therefore I used fastx-toolkit trimmer using the following code
fastx_trimmer -t 100 -Q33 -i file.fastq -o file_trimmed.fastq
although the files were sequenced quite recent, I needed to use the Q33 parameter, otherwise fastx_trimmer was not working.
Now I want to map these data using bwa-mem. I get however the following error message:
[mem_sam_pe] paired reads have different names: "M01441:126:000000000-ADL98:1:1104:10392:3758", "M01441:126:000000000-ADL98:1:1104:23060:3763"
So bwa-mem ended with an error. Does anyone know why this is happening and how to solve it?