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Forum: Illumina/Solexa 07-03-2018, 02:08 PM
Replies: 3
Views: 1,009
Posted By moatman
Does this relate to the first base(s) of the...

Does this relate to the first base(s) of the adapter in your sample sheet? I've run into that problem before, where adapter trimming will eat the last little bit, even if it happens to just be the...
Forum: Bioinformatics 03-05-2018, 01:29 PM
Replies: 6
Views: 1,060
Posted By moatman
As a side-note, when running bcl2fastq you can...

As a side-note, when running bcl2fastq you can use the option "--no-lane-splitting" to create fastqs that don't separate your samples by lane. This is useful to avoid having to combine them...
Forum: Illumina/Solexa 05-24-2017, 01:17 PM
Replies: 6
Views: 958
Posted By moatman
You can also tweak a file on the MiSeq to...

You can also tweak a file on the MiSeq to configure it to create index reads for every sample(and Undetermined) by following the guide here:...
Forum: Bioinformatics 12-13-2016, 08:13 AM
Replies: 9
Views: 1,103
Posted By moatman
We have a 2500 that was upgraded from a 2000 and...

We have a 2500 that was upgraded from a 2000 and we ran into issues using 1.8.4 and earlier to demux our runs, whereas 2 worked right out of the gate fairly smoothly for us.

I know that certain...
Forum: Bioinformatics 12-13-2016, 07:48 AM
Replies: 9
Views: 1,103
Posted By moatman
Is there any reason why you're using such an old...

Is there any reason why you're using such an old version of bcl2fastq? Last year they updated to bcl2fastq 2 and it runs much better. We previously had trouble demultiplexing hiseq runs with the...
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