I was asked to demultiplex a run where the samples had a unique i5 sequence but the i7 sequence was the same for all of them. I have tried to demultiplex it using several --use-bases-mask parameters but I cannot get it to work.
I tried to use
--use-bases-mask Y*,n*,I8n*,Y* and a samplesheet that looked like this:
I also tried to use
--use-bases-mask Y*,I8n*,I8n*,Y* and a samplesheet that looked like this:
None of these options worked for me. Is there a way to demultiplex that data?
I tried to omit it the first time because I was not told that it was dual indexed. The group has not given me their i7 indexes. If I ask for them and replace the NNNNNNNN with the sequence and use --use-bases-mask Y,I8n,I8n,Y would the demultiplexing work?
Correct. It will work.
Thank you for the help
Apparently they had not added the i7 indexes to the samples. Is there still a way to demultiplex it?
What do the indexes look like? There may be a dummy "TCTTTCCC" type sequence present in place of i7 indexes. You can simply add that in as i7 index even though it is not real.
Would the fragments attach to the flowcell if no p7 was added at all?
Is no sequence showing up if you simply use a dummy samplesheet with nothing in it so everything goes to "Undetermined"?
If the library was not properly made the run would have failed.
Would the run have failed even though there were 50 samples on that lane but only 6 were made without the p7? I could demultiplex the rest of the samples without any issue.
The run will not fail. Those 6 samples would not cluster thus will not be sequenced. Rest of the samples should be fine as long as they have proper adapters.