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Old 09-20-2016, 06:58 AM   #1
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Location: CT

Join Date: Apr 2015
Posts: 243
Default Basespace update

Illumina replaced MiSeq reporter as the demultiplexor for miseq data on basespace with bcl2fastq a couple of weeks ago. Since then I've run into a number of instances where MSR and bcl2fastq are different which had meant many demultiplexing failures. To save people time I thought I'd start the list of issues I've hit.

1. MSR allowed "." in sample names and sample ID, bcl2fastq does not

2. MSR treats "N" as wildcard, bcl2fastq treats it as exact. I run a mix of dual 8bp and TruSeq lt single index 6bp. MSR had allowed me to just put NNNNNNNN as the i5 and NN at the end of the i7, this no longer works. you have to use the actual sequences (AT at the end of i7 and TCTTTCCC for i5)

3. bcl2fastq or basespace is much much slower at demultiplexing. It used to take <30min to rerun a sample sheet, it's taking >4hours now.

4. bcl2fastq doesn't allow you to set the indexing mismatch (at least tech support that I talked to didn't know how to globally set). It tries to allow 1 mismatch and only drops to exact match if the hamming distance is <3
Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.

Last edited by thermophile; 09-20-2016 at 07:06 AM.
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