Nan Leng
`Hugo Lam
`Shujun Luo; John West; Christian Haudenschild; Mark Pratt; Christian Haudenschild; Richard Chen
`Re: MiSeq 2x250 run completed over the weekend
`Tuesday, August 28, 2012 10:19:14 AM
`
`From:
`To:
`Cc:
`Subject:
`Date:
`
`Hi All,
`
`I downloaded the 2x250 dataset from basespace into here /local/science-ops-
`1a/data/miseq/A1NGW/A1NGW_S0_L001_R1_001.fastq.gz
`
`I installed smalt which is the next generation aligner from Sanger after SSAHA2
`(http://www.sanger.ac.uk/resources/software/smalt/).
`time /home/nleng/bin/smalt-0.6.3/smalt_x86_64 map -i 800 -f samsoft -o map_1.sam -n 1
`/science/data/index/smalt/hg19 A1NGW_S0_L001_R1_001.fastq
`A1NGW_S0_L001_R2_001.fastq
`
`The initial quick test show smalt works. I got the map.sam file within 40min using 40core
`which is slower than BWA-SW. It will take roughly 24hrs to align 1x of 2x250. I am still
`testing this brand new aligner and will collect more stats later on.
`
`In the mean time, I will try to get MOSAIK and BFAST work.
`
`Thanks,
`
`Nan
`
`On 08/27/2012 11:26 AM, Hugo Lam wrote:
`
`Using BWA to align 1x of 2x300 took ~12 hrs. So a 40-core computer for a 40x
`2x250 will still take 10-12 hrs to finish the alignment. If we run the alignment on
`all 6 R910s we have, we can cut if down to less than 2 hrs for the alignment. Nan
`will be helping out on testing couple more aligners and we will have a better
`assessment on the alignment and its quality once he has finished it.
`
`On Mon, Aug 27, 2012 at 9:34 AM, Shujun Luo <shujun.luo@personalis.com>
`wrote:
`We got 3.1G for this run, and 2.4G with Q >30. Read1 error rate is 0.9 and read2 error rate
`is 1.44
`
`From: John West <john.west@personalis.com>
`
`Date: Monday, August 27, 2012 7:20 AM
`To: Microsoft Office User <shujun.luo@personalis.com>
`
`Cc: Christian Haudenschild <christian.haudenschild@personalis.com>, Mark Pratt
`<mark.pratt@personalis.com>, Christian Haudenschild
`<chaudenschild@personalis.com>, Nan Leng <nan.leng@personalis.com>, Richard
`
`Personalis EX2078.1
`
`
`Hugo Lam
`Shujun Luo; John West; Christian Haudenschild; Mark Pratt; Christian Haudenschild; Richard Chen
`Re: MiSeq 2x250 run completed over the weekend
`Tuesday, August 28, 2012 10:19:14 AM
`
`From:
`To:
`Cc:
`Subject:
`Date:
`
`Hi All,
`
`I downloaded the 2x250 dataset from basespace into here /local/science-ops-
`1a/data/miseq/A1NGW/A1NGW_S0_L001_R1_001.fastq.gz
`
`I installed smalt which is the next generation aligner from Sanger after SSAHA2
`(http://www.sanger.ac.uk/resources/software/smalt/).
`time /home/nleng/bin/smalt-0.6.3/smalt_x86_64 map -i 800 -f samsoft -o map_1.sam -n 1
`/science/data/index/smalt/hg19 A1NGW_S0_L001_R1_001.fastq
`A1NGW_S0_L001_R2_001.fastq
`
`The initial quick test show smalt works. I got the map.sam file within 40min using 40core
`which is slower than BWA-SW. It will take roughly 24hrs to align 1x of 2x250. I am still
`testing this brand new aligner and will collect more stats later on.
`
`In the mean time, I will try to get MOSAIK and BFAST work.
`
`Thanks,
`
`Nan
`
`On 08/27/2012 11:26 AM, Hugo Lam wrote:
`
`Using BWA to align 1x of 2x300 took ~12 hrs. So a 40-core computer for a 40x
`2x250 will still take 10-12 hrs to finish the alignment. If we run the alignment on
`all 6 R910s we have, we can cut if down to less than 2 hrs for the alignment. Nan
`will be helping out on testing couple more aligners and we will have a better
`assessment on the alignment and its quality once he has finished it.
`
`On Mon, Aug 27, 2012 at 9:34 AM, Shujun Luo <shujun.luo@personalis.com>
`wrote:
`We got 3.1G for this run, and 2.4G with Q >30. Read1 error rate is 0.9 and read2 error rate
`is 1.44
`
`From: John West <john.west@personalis.com>
`
`Date: Monday, August 27, 2012 7:20 AM
`To: Microsoft Office User <shujun.luo@personalis.com>
`
`Cc: Christian Haudenschild <christian.haudenschild@personalis.com>, Mark Pratt
`<mark.pratt@personalis.com>, Christian Haudenschild
`<chaudenschild@personalis.com>, Nan Leng <nan.leng@personalis.com>, Richard
`
`Personalis EX2078.1
`
`
`
`Chen <richard.chen@personalis.com>, Hugo Lam <hugo.lam@personalis.com>
`Subject: MiSeq 2x250 run completed over the weekend
`
`All,
`
`This was our first run with Illumina's newest sequencing biochemistry, rumored to have a
`new & better polymerase. They have released it on the MiSeq first and, as I understand it,
`plan a HiSeq version later this year, but only 2x150 bases there.
`
`Shujun :
` How many raw G bases resulted from this run ?
` Is there a run # we can refer to it by ?
`
`Nan :
` Can you please download this from BaseSpace, convert the raw data (no GATK Q-score
`recalibration) to a SAM file and put it on a memory stick for me ? I will give you a memory
`stick for this when I get in.
`
`Also, can you run the QC tool on this and circulate the result ? I am particularly interested
`in the GC bias.
`
`Christian :
` Do you know when our MiSeq will be upgraded to dual-surface imaging, which should
`double it's yield per run ?
`
`Hugo :
` What are your thoughts on alignment of this longer read data ?
`
`Thanks,
`
`John West
`
`Cell (408) 836-5586
`jwest38261@aol.com
`
`On Aug 26, 2012, at 11:07 PM, Shujun Luo <shujun.luo@personalis.com> wrote:
`
`Hi John,
`
`We have the most updated chemistry for HiSeq, i.e., PCR free gel free sample
`prep, v3 cluster and sequencing chemistry.
`
`I just finished one 2x250 miseq run with the new sequencing reagent, with
`the PCR free gel free Amy library. The seq matrix looks good. The data is
`
`Personalis EX2078.2
`
`
`
`available at our basespace account. For some reason, there is no alignment
`data on basespace any more, and we will do a local alignment tomorrow.
`
`Thanks,
`
`Shujun
`
`From: John West <john.west@personalis.com>
`Date: Sunday, August 26, 2012 9:51 PM
`To: Christian Haudenschild <christian.haudenschild@personalis.com>
`Cc: Mark Pratt <mark.pratt@personalis.com>, Microsoft Office User
`<shujun.luo@personalis.com>, Christian Haudenschild
`<chaudenschild@personalis.com>
`Subject: Re: Newest reagents for HiSeq operation
`
`Hi Christian,
`
`I think the SRA data we downloaded earlier this year might
`have been PCR-free but not gel-free ? Mark ?
`
`It would be great to try a MiSeq 2x250 Amy genome. Do we have the best
`library for that ? Would that be PCR-free gel-free too?
`
`Thanks,
`
`John West
`
`Cell (408) 836-5586
`jwest38261@aol.com
`
`On Aug 26, 2012, at 9:35 PM, Christian Haudenschild
`<christian.haudenschild@personalis.com> wrote:
`
`The data downloaded from illumina that is from january was
`V3 and no PCR I believe.
`We are only running V3.
`We have or should have received V2 miseq on Friday, so we
`could try a real 2X250 and see where it gets us, illumina
`upgraded the miseq software on thursday.
`Christian.
`
`From: John West <john.west@personalis.com>
`Date: Sunday, August 26, 2012 8:57 PM
`
`Personalis EX2078.3
`
`
`
`To: Mark Pratt <mark.pratt@personalis.com>, shujun luo
`<shujun.luo@personalis.com>, Christian Haudenschild
`<chaudenschild@personalis.com>
`Subject: Newest reagents for HiSeq operation
`
`Mark, Shujun, Christian,
`
`I have been discussing with Mark how to use the results of our
`A/B comparisons to direct our development of accuracy-
`improving sample preps and bioinformatics. He has pointed
`out that the A/B comparisons we have so far are based on data
`from the Broad, using v2 Illumina sequencing chemistry. Now
`there is not only a v3 sequencing chemistry, but as I
`understand it, also a TruSeq PE Cluster kit v3-cBot-HS, which is
`supposed to significantly reduce GC-bias induced at high
`cluster density. On the Illumina web site, some of that seems
`to be fairly new, but it is a little hard to tell. For our in-house
`HiSeq runs, do we have these newest reagents ? It is pretty
`important for us to move our analysis forward from v2. If we
`do not have them yet, do we know when we will ? I am also
`not sure if we are following the gel-free PCR-free library prep
`protocols, or if there are issues with them ? They are also
`supposed to help a lot in reducing GC-bias.
`
`Perhaps we can meet briefly Monday to discuss the next HiSeq
`run.
`
`Thanks,
`
`John
`
`--
`Hugo Lam, PhD
`Project Manager, Computational Biology
`Personalis Inc.
`http://www.personalis.com/
`
`Personalis EX2078.4
`
`
Accessing this document will incur an additional charge of $.
After purchase, you can access this document again without charge.
Accept $ Charge
Still Working On It
This document is taking longer than usual to download. This can happen if we need to contact the court directly to obtain the document and their servers are running slowly.
Give it another minute or two to complete, and then try the refresh button.
A few More Minutes ... Still Working
It can take up to 5 minutes for us to download a document if the court servers are running slowly.
Thank you for your continued patience.
This document could not be displayed.
We could not find this document within its docket. Please go back to the docket page and check the link. If that does not work, go back to the docket and refresh it to pull the newest information.
Your account does not support viewing this document.
You need a Paid Account to view this document. Click here to change your account type.
Your account does not support viewing this document.
Set your membership
status to view this document.
With a Docket Alarm membership, you'll
get a whole lot more, including:
- Up-to-date information for this case.
- Email alerts whenever there is an update.
- Full text search for other cases.
- Get email alerts whenever a new case matches your search.
One Moment Please
The filing “” is large (MB) and is being downloaded.
Please refresh this page in a few minutes to see if the filing has been downloaded. The filing will also be emailed to you when the download completes.
Your document is on its way!
If you do not receive the document in five minutes, contact support at support@docketalarm.com.
Sealed Document
We are unable to display this document, it may be under a court ordered seal.
If you have proper credentials to access the file, you may proceed directly to the court's system using your government issued username and password.
Access Government Site
