Moving to bsky.app/profile/eric-c…. See you all on the other side!
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CAT at UCSF
237 posts
CAT at UCSF
@CAT_UCSF
The Center for Advanced Technology brings the latest tech to researchers @UCSF and beyond.
San Francisco, CA Sumali Mart 2015
157 Sinusundan344 Mga Tagasunod
Our updated website is now live (cat.ucsf.edu) and more updates will be added in the upcoming weeks.
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@CatharineAquino I don’t think he’s referring to that because Element kits also come kitted in specific cycle numbers like the NovaSeq. You can’t just substitute several 50 cycle kits for a 200 or 300 cycle kit like we could with the HiSeq.
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The read configuration can be customized with the Novaseq/NS2000. Or is he referring to the HiSeq days when the reagents came in 250ml bottles and can be combined and every drop can be used?
Albert Vilella@AlbertVilella
like the order and number of cycles of R1 and R2 reads, the length of the cycles, etc. But all of these kind of disappeared with the NovaSeq/NextSeq2000 era of instruments, instead Illumina offering customers a set of kits to cater for "all" their needs.
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This is incorrect. You can enter in custom cycle parameters for all the @illumina sequencers (not sure about the Dx versions). For example on the NovaSeqX we do SE100, PE50, and @10xGenomics specific scRNA parameters and on the NovaSeq6k, we did a ~300 base R2 on an S4.
Albert Vilella@AlbertVilella
like the order and number of cycles of R1 and R2 reads, the length of the cycles, etc. But all of these kind of disappeared with the NovaSeq/NextSeq2000 era of instruments, instead Illumina offering customers a set of kits to cater for "all" their needs.
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@CuylerLuck @hitenmadhani We don’t offer library prep, just by the lane sequencing (PE150, PE50, SE100, 10X RNA/Visium). These rates should be cost competitive with any other option.
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We excited to offer @PacBio Revio sequencing for the @UCSF community. A launch party is happening this Wednesday (9/27) from 12-2pm in HD160. Register here: programs.pacb.com/l/1652/2023-08…
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@jdidion @bossuyt_wouter @OmicsOmicsBlog @illumina 15% < Q30 And 3Tb are the minimum specs. System often exceeds this yield and quality, but agree, axes would be nice. Also since this was probably a well-characterized genome, would be great to see how accurate QScores are above 40.
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@bossuyt_wouter @OmicsOmicsBlog @illumina If I read the slide right, 2.4/3TB = 80% Q40. And there’s 15% < Q30, leaving 5% in the Q30-39 bin, which in the plot is 2-3x larger than the <Q30 bin.
Or is the implication that the spec is 85% Q30 but you actually see a lot less in that bin? Axes would help :)
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@oweissb Most of this is likely the PhiX spike-in. Illumina PhiX libraries don’t contain a full index read 1 primer binding site so they show up as a run of G’s on 2-color systems. You can test this by aligning the undetermined file against PhiX.
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Hi people doing sequencing analysis, we have a question. Whenever we run multiplex sequencing on a NovaSeq, we get a huge number of reads (100 million) that can't be demultiplexed (barcode=GGGGGG). Does anyone else have this issue?
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NovaSeqX validation run went great! We averaged 12.5B clusters/FC, 7.4Tb total, >94% Q30. Let’s see what happens with other validation runs! #NovaSeqXCup? Next step training. Stay tuned!
BKahl@BrendaKahl5
There's a lot of smiling faces as another #NovaSeqX is installed @CAT_USCF. Can't wait to see the output of the first run. @illumina the bar has been set high yet again!
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We've had a great experience with our previous Illumina sequencers. Nearly 2000 runs on our 4000 and about 1500 runs on our 6000s. Looking forward to seeing how many we can rack up on the X. We'll post more info as we finish validation and deploy the X for production.
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We're hoping to begin sequencing soon with SE100, 10xRNA, PE50/10x ATAC lanes on the 100 cycle kit and PE150 runs on the 300 cycle kit. Expect 1.25B reads per lane on the 10B kits. We're really excited to have a replacement for the trusty HiSeq 4000 for shorter single end runs.
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CAT at UCSF nag-retweet
Interested in learning more about #3DGenomics? We'll be on @UCSF's campus hosting two lunch and learns on Monday! Register below and bring lots of questions:
Parnassus Campus: hubs.la/Q01s6VlH0
Mission Bay Campus: hubs.la/Q01s6X530
@NadavAhituv @ElphegeNoraLab
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@hitenmadhani We’ve been using @Agilent pools and they have been great. Is there a reason you go with Genescript?
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@Ali_SyedRaza If you are using dual index libraries and v1 NovaSeq reagents, no change needed, but most groups are using v1.5 reagents. In this case you’ll need to reverse complements the second index. More info: support-docs.illumina.com/SHARE/IndexedS…
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@Ali_SyedRaza Depends on if you are using single or dual indexed libraries and if you are using v1 or v1.5 NovaSeq reagents. If you are using single index libraries, no change is needed.
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Have a quick question for scRNA-aficionados: Miseq was done for the same batch of samples followed by Novaseq, one would expect the sample sheet for both the runs to be same??! Sample indexing is the same. Sample sheet as in for generation of FASTQ files from the BCL output.
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@AntoBeck @Genomics_Guy @illumina Is ~2 years the expected shelf life? The lot and serial numbers don’t seem real.
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