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Forum: Illumina/Solexa 02-10-2021, 06:38 PM
Replies: 2
Views: 445
Posted By kcchan
bcl-convert installs just fine in Ubuntu. The...

bcl-convert installs just fine in Ubuntu. The process is the same as installing bcl2fastq2

About 90% of the features from bcl2fastq were missing until the most recent release, but now it's mostly...
Forum: Illumina/Solexa 02-28-2020, 11:12 AM
Replies: 4
Views: 2,234
Posted By kcchan
Illumina just posted two sample runs on...

Illumina just posted two sample runs on BaseSpace. You should be able to download the data and see for yourself.

https://basespace.illumina.com/datacentral
Forum: Illumina/Solexa 12-05-2019, 02:50 PM
Replies: 6
Views: 3,209
Posted By kcchan
Have you tried upgrading bcl2fastq v2.20? v2.19...

Have you tried upgrading bcl2fastq v2.20? v2.19 was really buggy for NovaSeq data
Forum: Illumina/Solexa 06-19-2018, 10:59 PM
Replies: 2
Views: 1,937
Posted By kcchan
This tech support bulletin might be useful:...

This tech support bulletin might be useful: https://support.illumina.com/bulletins/2017/02/options-for-downloading-run-folders-from-basespace-sequence-hub.html
Forum: Illumina/Solexa 05-08-2018, 06:19 PM
Replies: 5
Views: 1,807
Posted By kcchan
Are you sure the 300bp was the insert size and...

Are you sure the 300bp was the insert size and not the total fragment size? The adapters add about 150bp to the total fragment size so this looks about right in that case. The asymmetric distribution...
Forum: Illumina/Solexa 10-10-2017, 01:44 PM
Replies: 26
Views: 11,672
Posted By kcchan
How did you come up with that 10^-6 figure? In an...

How did you come up with that 10^-6 figure? In an RNASeq or CHIPseq experiment that's only about 20-30 reads.
Forum: Illumina/Solexa 10-06-2017, 10:53 AM
Replies: 26
Views: 11,672
Posted By kcchan
Honestly this index hopping issue is way...

Honestly this index hopping issue is way overblown. For most sequencing applications it's a non-issue. From our experience a clean library (i.e. no visible primers or dimers in BA trace), the hopping...
Forum: Illumina/Solexa 09-29-2017, 12:34 PM
Replies: 4
Views: 1,118
Posted By kcchan
A lot of the leftover reagents is actually water...

A lot of the leftover reagents is actually water from the template rinse and back flush. Probably not a good idea to re-use them.
Forum: Illumina/Solexa 07-17-2017, 12:38 PM
Replies: 3
Views: 4,914
Posted By kcchan
Did you remember to reverse complement the...

Did you remember to reverse complement the index2s?
Forum: Illumina/Solexa 06-29-2017, 09:27 PM
Replies: 3
Views: 1,576
Posted By kcchan
The HiSeq 2000s were finicky at start up. You...

The HiSeq 2000s were finicky at start up. You have to wait until the "DONOTEJECT" drive initializes before starting HCS. Otherwise you get that error.
Forum: Illumina/Solexa 05-12-2017, 10:25 AM
Replies: 12
Views: 2,196
Posted By kcchan
Like GenoMax says it depends on the setup of the...

Like GenoMax says it depends on the setup of the individual facility. For a core lab or service provider it makes sense to keep all the raw data in case customers need to have their data...
Forum: Illumina/Solexa 05-11-2017, 08:09 AM
Replies: 12
Views: 2,196
Posted By kcchan
Sorry I was referring to 10-15 Gigabytes of data,...

Sorry I was referring to 10-15 Gigabytes of data, which includes all the FASTQs, bcls, and thumbnails.
Forum: Illumina/Solexa 05-10-2017, 06:15 PM
Replies: 12
Views: 2,196
Posted By kcchan
The computer is buried inside the instrument and...

The computer is buried inside the instrument and is definitely not user accessible. Opening it up is probably going to void your warranty.

You can change the config settings to output the data...
Forum: Illumina/Solexa 10-14-2016, 09:57 AM
Replies: 10
Views: 3,053
Posted By kcchan
From my experience it works just fine on NextSeq...

From my experience it works just fine on NextSeq runs. The intensity metrics are a little funny due to the 2 color chemistry but other than that there shouldn't be any problems.
Forum: Illumina/Solexa 09-26-2016, 04:21 PM
Replies: 28
Views: 5,765
Posted By kcchan
There is a message where the "Launch App" button...

There is a message where the "Launch App" button used to be:



This includes all published apps as well as any custom apps you have in your developer account.
Forum: Illumina/Solexa 09-23-2016, 10:00 AM
Replies: 28
Views: 5,765
Posted By kcchan
That issue still hasn't been fixed as of the the...

That issue still hasn't been fixed as of the the most recent 2.18 update.
Forum: Illumina/Solexa 09-20-2016, 06:53 PM
Replies: 28
Views: 5,765
Posted By kcchan
I would imagine some of the third party...

I would imagine some of the third party developers aren't too happy either since their apps are now stuck behind a paywall.
Forum: Illumina/Solexa 09-20-2016, 12:14 PM
Replies: 28
Views: 5,765
Posted By kcchan
In addition the BaseSpace apps are no longer...

In addition the BaseSpace apps are no longer free. You now must be subscribed to a Professional account to access the apps and also pay each time you run them.
Forum: Illumina/Solexa 09-14-2016, 04:21 PM
Replies: 9
Views: 3,182
Posted By kcchan
From the Illumina FAQ:

From the Illumina FAQ:
Forum: Illumina/Solexa 10-22-2015, 11:23 AM
Replies: 2
Views: 1,563
Posted By kcchan
Almost all of that volume is water from the...

Almost all of that volume is water from the template rinse.
Forum: Illumina/Solexa 04-26-2015, 11:17 PM
Replies: 26
Views: 12,362
Posted By kcchan
You have to go into the Sample section (tube icon...

You have to go into the Sample section (tube icon on the left sidebar) and click on the file name for each file (and not the checkbox). It will give you the error message "File is either not...
Forum: Illumina/Solexa 04-24-2015, 06:38 PM
Replies: 26
Views: 12,362
Posted By kcchan
It's still possible to download files without...

It's still possible to download files without their download program. You will need to go into each file and download them one by one.
Forum: Illumina/Solexa 02-19-2015, 10:24 AM
Replies: 6
Views: 2,952
Posted By kcchan
You'll likely only be able to keep track of the...

You'll likely only be able to keep track of the service providers and university core labs who advertise that they have sequencing capabilities. As sequencers get cheaper a lot of smaller labs and...
Forum: Illumina/Solexa 01-26-2015, 12:56 PM
Replies: 53
Views: 88,351
Posted By kcchan
The difference is even less if you compare HiSeq...

The difference is even less if you compare HiSeq 2500 V4 to HiSeq 4000. The HiSeq 4000's specs claim 4.3-5B reads vs up to 4B reads on a HiSeq 2500. After factoring in instrument and overhead costs I...
Forum: Illumina/Solexa 01-16-2015, 03:06 PM
Replies: 3
Views: 1,890
Posted By kcchan
If the headers are starting with @HWI it's almost...

If the headers are starting with @HWI it's almost certainly generated using BCL2FASTQ and not MiSeq Reporter, which uses @M0xxxx.
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