I have some paired end illumina fastq files. In most of these the sequence identifiers are like this:
.... @GENOTEK:000:311CE525F:3:1101:17996:1000 1:N:0:TCTTCACA+ATTACTCG @GENOTEK:000:311CE525F:3:1101:21938:1000 1:N:0:TCTTCACA+ATTACTCG @GENOTEK:000:311CE525F:3:1101:1208:1016 1:N:0:TCTTCACA+ATTACTCG @GENOTEK:000:311CE525F:3:1101:3558:1016 1:N:0:TCTTCACA+ATTACTCG ....
So as i can understand TCTTCACA+ATTACTCG constitutes first and second index primers which are attached to the fragment to differentiate one end from another.
But at least one pair of files has identifiers like this:
.... @GENOTEK:000:9589D2457:7:1101:12895:1362 1:N:0:NTTACTCG @GENOTEK:000:9589D2457:7:1101:16011:1379 1:N:0:NTTACTCG @GENOTEK:000:9589D2457:7:1101:17381:1432 1:N:0:NTTACTCG .... .... @GENOTEK:000:9589D2457:7:1101:12895:1362 2:N:0:NTTACTCG @GENOTEK:000:9589D2457:7:1101:16011:1379 2:N:0:NTTACTCG @GENOTEK:000:9589D2457:7:1101:17381:1432 2:N:0:NTTACTCG ....
So it contains only one index primer, and moreover, it is equal at both ends. Does it mean it is impossible to distinguish one end of the fragment from another, so these are effectively single end reads?
And also all the files have run number 000. Is it the thing to worry about?
Thanks in advance.