I have downloaded the fastq files for paired end RNA-sequencing for a single cell line from the ENCODE project, as I want to map the reads my self in the search for chimeric read pairs.
My problem is that for each sample, the read1 and read 2 fastq.tgz folders contain 5 separate fastq-files. Should these files be merged before or midway in my mapping? If yes - how?
My problem is that for each sample, the read1 and read 2 fastq.tgz folders contain 5 separate fastq-files. Should these files be merged before or midway in my mapping? If yes - how?
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