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The run is a pair-end run with 2*36 cycles. Firstly, one direction reads were obtained through the RTA process but the samba server shut down when the RTA running for another direction reads. I do the image analysis using "goat_pipeline.py" for the rest image to get these reads named "s_x_1_xxxx_qseq.txt" and put the former reads renamed "s_x_2_xxxx_qseq.txt" into the same directory.
Then I would do the rest analysis using the "GERALD.pl". But the pipeline can't recognize the PE data, it regards the data as a single run.
I have contacted the engineer of illumina, but the problem can't be solved up to now.
Please show me some guidance
Then I would do the rest analysis using the "GERALD.pl". But the pipeline can't recognize the PE data, it regards the data as a single run.
I have contacted the engineer of illumina, but the problem can't be solved up to now.
Please show me some guidance