CAT at UCSF

The Center for Advanced Technology brings the latest tech to researchers @UCSF and beyond.

[CAT at UCSF @CAT_UCSF]

Moving to https://t.co/WGUVLD275f. See you all on the other side!

[CAT at UCSF @CAT_UCSF]

@OmicsOmicsBlog I hope this was a joke. If not 🤦‍♂️

[CAT at UCSF @CAT_UCSF]

Our updated website is now live (https://t.co/5xzVa0caoI) and more updates will be added in the upcoming weeks.

[CAT at UCSF @CAT_UCSF]

@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.

[CAT at UCSF @CAT_UCSF]

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.

[CAT at UCSF @CAT_UCSF]

@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.

[CAT at UCSF @CAT_UCSF]

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: https://t.co/6esRMmoDLg

[CAT at UCSF @CAT_UCSF]

@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.

[CAT at UCSF @CAT_UCSF]

@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.

[CAT at UCSF @CAT_UCSF]

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!

[CAT at UCSF @CAT_UCSF]

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.

[CAT at UCSF @CAT_UCSF]

We're excited that our @illumina #NovaSeqX was installed last week. This system will benefit a wide range of projects for our @UCSF research community. Validations runs are should be starting later today.

[CAT at UCSF @CAT_UCSF]

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.

[Arima Genomics @ArimaGenomics]

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: https://t.co/jtVPLE4z42
Mission Bay Campus: https://t.co/05a6fDmhkW

@NadavAhituv @ElphegeNoraLab

[CAT at UCSF @CAT_UCSF]

@hitenmadhani We’ve been using @Agilent pools and they have been great. Is there a reason you go with Genescript?

[CAT at UCSF @CAT_UCSF]

@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: https://t.co/ls8n2EsBnQ

[CAT at UCSF @CAT_UCSF]

@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.

[CAT at UCSF @CAT_UCSF]

@AntoBeck @Genomics_Guy @illumina Is ~2 years the expected shelf life? The lot and serial numbers don’t seem real.