I have received data files from a Solexa run done elsewhere--have no familiarity with output files, but understand that paired end reads should be identifiable by /1 and /2 at the end of the FASTQ defline. All end with /1. Does this mean the run was analyzed as if unpaired reads or should there be a second file of reads? Would all /1 reads start from the same primer ("A") and all /2 from "B"? Thanks in advance. The run was 2x56, paired ends.
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It sounds like you've been given either one half of the pairs, or single read data. Are all the reads the right length?
Normally you'd have two files - one containing all the sequences from the first read and the second containing their pairs. They're often called something along the lines of
s_4_2_sequence.txt
The '4' refers to lane 4 of the flowcell, and the '2' means the second read. So in this instance if it was paired-read data, you'd have:
s_4_1_sequence.txt (with /1 in the read names)
s_4_2_sequence.txt (with /2 in the read names)
Of course, your sequence provider may rename them to something else.
Cheers,
Scott. -
You can double check this by looking at the x-y coordinates in the read names. A read name looks like <run>:<lane>:<tile>:<x>:<y>/<read>, or for example 'IL16_3243:4:10:17:1030/1'. If what you have really is two files containing matching paired end reads, the lane/tile/x/y information should be the same in both -- and normally in the same order, so the files match read-for-read. If that's true, the read number just got messed up. Otherwise, you've got something else.
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