Question: Why does the longranger basic pipeline only output one FASTQ file when I gave it paired-end data?
Answer: The default output of the longranger basic pipeline is an interleaved FASTQ file. An interleaved FASTQ file has both read pairs in the same file, where read 1 comes first and read 2 immediately follows. Here is an example:
@ST-E00273:259:H7WY3ALXX:1:1101:15554:38315 BX:Z:AAACACCAGCGATATA-1 TTGTTGTTCTTAACATTTCTGTTGATTCAGGTAAGTTCCATTGGCATTTCAGTACAACTAGTGACTAATGCCTCAAAGAATGAAATGAAATTCTACAGCTCTGCTATGACTGGAATGAGATAACAGTT + JJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJF-FFJJJJJJFJJJJFJJJJJJFFFJJJJJFJJJJJJJJJFJJFFJJJJJ--7<AFJ<FJFAFFJJJJ-AJJ<JFJJJA-7FF7AJAA<F7--<-7- @ST-E00273:259:H7WY3ALXX:1:1101:15554:38315 BX:Z:AAACACCAGCGATATA-1 ACCAAGGGAGAAAGTAGATGAAATGTTCTTCTACTTTCTCCCTTGGTTGACATTAAAAAAAATTACATGTTCCGAACAAGATAATTGACATAGGCTCAAGTAGAAGGCGGGAACTCTGGTTAAAAAAAAAAAAATGAAAGCGCCAGCCCGG + AAFFFJFJJJJJJJJJJ<JJJJFJJJJAJJJJFJJJJFJJJJFJJJJAJJ<-F7J<7FF-7-<FJ<JF7--A---AAAF-7-7F-<-A-<77-7-7---A-7<A<-AFJF-AF7-7--7--7<<7------------7A---7)-))-)))
You can see that read 1 is shorter than read 2 because the barcode has been removed. The barcode is added as a BX: comment on the ID line of both reads. For an explanation of why some reads will not have a BX: comment please see this article: Why do some of the processed reads from the Long Ranger Basic pipeline not have barcodes associated with them?