The data was generated in MiSeq , demux was done in LRM but it didn't yeild any data assigned to the sample, but the other issue is in the undermined files we are not able to see in any index in the header of the undermined fastq files, which seems bit strange.
Any suggestion how to troubleshoot ,since SAV looks all fine the index read have good Q30 scores as adding the information
zcat Undetermined_S0_L001_R1_001.fastq.gz | head
@M06594:100:000000000-DN78N:1:1101:16087:1338 1:N:0:0
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTNNNNNTTTTTTTTTNNNNNNNNTTTTTTTTNNTTTTTTTTTTTT
+
1111>1>10000AA//AA/>///////<<<</<//-------:-9-9-9-999-9--9-9-9-9-------9-9-999-9-9--9------9-----99--9---#:#####99--9----########--999---##9----9----99
@M06594:100:000000000-DN78N:1:1101:15529:1349 1:N:0:0
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNTTTTTTTTTTTTTTTTTTTTTT
+
11111>1>>>>0///AA/////>////<<//////--<<-----9-9--9---9----99----9-999--999-------99//999:-9-99-------999----;---9--------########-----;---99-----9---9-
@M06594:100:000000000-DN78N:1:1101:15215:1371 1:N:0:0
Any suggestion how to troubleshoot, what could be the issue?
yes 15% phix was spiked in, now since that was in LRM i did try in bcl2fastq i can see the index in the header but no difference in the output . I did try swapping the index, then Reverse compliment the i5 index but no difference as such.