Please somebody help me,
I have fastq.gz files of three different groups of experiment from NextSeq 550 through BD rhapsody WTA multiplex pipeline.
I tried to analyze those results on SevenBridges using BD WTA pipeline but only one of three groups was successful and other groups have failed.
I asked for support and was told that pair fastq files (R1 and R2) have different lines so I counted line using 'wc -l' function and divided by four.
The number of line was similar in successful group however the other failed group showed big differences.
Does anyone know what to do with fastq.gz files to run the analysis pipeline successfully?