Miseq Index file Mismatch

[emilyj]

Hello,

I have a Miseq Barcode library run that I am trying to use idemp to demultiplex using the I1.fastq index file from the instrument. However, the read names do not match up to my R1 read set:

Read names are different at read 17393140 between files
AF015_S1_L001_I1_001.fastq AF015_S1_L001_R1_001.fastq
M04872:20:000000000-BH9GY:1:2114:17482:28493
M04872:20:000000000-BH9GY:1:2114:17481:28493


Any reason for this? And how to fix it?

[GenoMax]

Was the data trimmed on the sequencer?

May want to give sabre (https://github.com/najoshi/sabre) a try.

[emilyj]

They have not been processed other than converting the bcl to fastq via miseq reporter. The index file was from the sequencer but the read files were converted to fastq on BaseSpace. Perhaps that is part of the problem, I am transferring the raw reads from the instrument now to see.