Question: bcl to fastq
gravatar for Jess
9 months ago by
Jess0 wrote:


We are using an Illumina MiSeq machine. Sample sheet generation using Illumina’s software is a lot of work so we just made our own layout in excel which finished sample sheet is the same as Illumina’s (in csv format). It just so happened that in our latest run the header of index i7 which is supposed to be “index” was changed to “index1”. And this caused the bcl files not to be demultiplexed to fastqs. Also, there is no read for this index in the MiSeq output-- there only 3 reads wherein there should be 4 reads. Is there still a way to demultiplex it on the MiSeq Control Software, like editing the sample sheet or the runinfo.xml file?

miseq next-gen • 382 views
ADD COMMENTlink modified 9 months ago by finswimmer12k • written 9 months ago by Jess0

Though it is not the proper solution. I think you can try taking undetermined reads left after demultiplexing of 3 samples as data for your 4 sample. If you have added PhiX Control then you can map undetermined reads to PhiX genome and can work with remaining data.

ADD REPLYlink written 9 months ago by toralmanvar820
gravatar for finswimmer
9 months ago by
finswimmer12k wrote:


you can simply edit the SampleSheet in the Analysis folder and requeue it.

A second choice is to install bcl2fastq and use it for demultiplexing.

fin swimmer

ADD COMMENTlink written 9 months ago by finswimmer12k


I edited the samplesheet-- changed "index1" to "index" but it still didn't work. I think the only way to demultiplex it is by using bcl2fastq or other means. since there are no reads generated for index 1 (index i7). If you have any other suggestions please let me know. Also, can I install bcl2fastq offline?

Thanks for the help!

ADD REPLYlink written 9 months ago by Jess0

yes, you can download bcl2fastq from here and can install it offline.

ADD REPLYlink written 9 months ago by toralmanvar820
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