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Tech Memosequencing analysis pipeline on cloud computing
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sequencing analysis pipeline on cloud computing
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sequencing analysis pipeline on cloud computing
arcadiac.blogspot.com
Tech Memo: October 2007
http://arcadiac.blogspot.com/2007_10_01_archive.html
Recommended settings for Windows 2000 / XP. Windows 2000 and XP, unlike NT supports large windows as described in RFC1323 ( the 'RcvWindow' has a maximum value of 2* 30 rather than 64K), and includes some other improvements over its predecessors you can use to speed up any TCP/IP transfers. The best settings are listed in red, the descriptions and other options are added to provide you with better understanding and enable you to customize your settings. DWORD, number of bytes) Valid range is from MSS to ...
Tech Memo: Sample Unix/Linux Commands
http://arcadiac.blogspot.com/2010/06/sample-unixlinux-commands.html
Search text "abc" under . recursively (-r) and show file names (-H). Grep -H -r "abc" . Search files by name, and delete them all. Find / -name *.log -exec rm {} ; OR. For f in `find / -name *.log`; do rm "$f" done. Sort fileA fileB uniq -u. Tr -s ' n'. Sort -t$' t' file. Subscribe to: Post Comments (Atom). DB2 CLI ODBC windows MS. Copy and paste worksheets. Picture Window template. Powered by Blogger.
Tech Memo: Reorder BAM files for GATK
http://arcadiac.blogspot.com/2013/04/reorder-bam-for-gatk.html
Reorder BAM files for GATK. GATK requires the input BAM file to be sorted in the same way as the reference (e.g., chr1/chrM first), but some BAM files are lexicographically sorted (e.g., chr10 first). Java -Xms2G -jar ReorderSam.jar I=in.bam O=out.bam REFERENCE=hg19.fasta VALIDATION STRINGENCY=LENIENT CREATE INDEX=true CREATE MD5 FILE=true. Without validation option, "MAPQ muse be 0 for unmapped read". Errors may appear (and stop). If missed, index file can be created with Samtools. From BAM to FASTQ.
Tech Memo: November 2009
http://arcadiac.blogspot.com/2009_11_01_archive.html
Cygwin 1.7 errors on Windows 7 64bit. I didn't get any trouble during installation, but many spurious errors including heap allocation problems popped up after that. 1 re-installation from cygwin 1.5 to 1.7. 2 setup environment variables. Set %TMP% directory writable from cygwin mode. 3 change cygwin max memory (following this guide. 5 set malloc related programs (sh, bash, make, .) running under XP SP2 compatibility mode. 6 using 32bit version cmd.exe (%WINDOWS% syswow64 cmd.exe). Labels: cygwin 1.7.
Tech Memo: April 2013
http://arcadiac.blogspot.com/2013_04_01_archive.html
From BAM to FASTQ. Java -Xms4G -Xmx8G -jar SamToFastq.jar INPUT=in.bam FASTQ=in.fq1 SECOND END FASTQ=in.fq2 VALIDATION STRINGENCY=LENIENT. Took about 8 hours. Throw " Found 24567 unpaired mates. Exception, but got FASTQ files anyway. Java -Xms8G -Xmx32G -jar gatk.jar -T CallableLoci -R hg19.fasta -I my.bam -summary my.summary -o my.bed. Need index file ( my.bai. In the same directory. Took about 7 hours per genome ( 90GB). Reference base was N! LOW COVERAGE 37531187 # Less than - minDepth. 4) read at loci.
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arcadiabusinesslaw.wikispaces.com
ArcadiaBusinessLaw - home
Skip to main content. Unit 1 - Our Legal System. Unit 2 - Entering Into Contracts. Unit 3 Beyond Contracts. Welcome to Business Law! If you are tardy, you will have to serve time after school after the first one. Bring your textbook every day. Be respectful of the opinions and people around you. Be responsible by turning in homework when assigned. My name is Peg Baumgartner, I have been teaching in Arcadia for over ten years! How to Use this Site. How to Use the Discussion Tab. Go to the Discussion Tab.
Arcadia Business Park - Warehouse / Showroom Leasing
Warehouse and showroom space for Lease. 4075 South Arcadia Lane, Fort Mohave, AZ 86426. Looking for showroom or warehouse space? We have units from 1,000 to 6,000 square feet available for immediate occupancy. We offer both short and long term leases with low lease rates. The Arcadia Business Park is located in western Arizona, near the California and Nevada borders. Our facility is 1 block west of Highway 95 at 4075 South Arcadia Lane, Fort Mohave, Arizona. Click here for a map. South Arcadia Lane - -.
Arcadia Buyer Rebates
South West - Sarasota. South East - Miami. Central West - Tampa. Central East - Daytona Beach. Savvy Arcadia Home Buyers Save Thousands! Most folks have never heard of real estate commission rebates. But Florida home buyers can save thousands of dollars with this well-kept secret. If you, a friend or family member is considering the purchase of a Arcadia. Condo, for example, and the anticipated sales price is $400,000, the rebate would equal $6000! 400,000 x 1.5% = $6000. It's that simple. Registration m...
Tech Memo
Problem: Cygwin xterm starts with sh, not bash. File exists: if not, add these lines in the file. Etc/shells: valid login shells. Rsync -avP - inplace -e "ssh -c arcfour" src [user@]host:/dir/to/target/. Preserve group (-g) option included in archive (-a) may not work well with remote site: -vrlptoDP instead. Source: http:/ blog.dnaseq.org/2013/01/blazing-fast-file-transfer-with-rsync.html. From BAM to FASTQ. Took about 8 hours. Throw " Found 24567 unpaired mates. Exception, but got FASTQ files anyway.
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C3 zoned property in Columbia, Missouri - Home
In Columbia, Missouri. Over 17 acres of C3-zoned property are now easily accessible from an easy to navigate clover-leaf interchange on US 63 opposite the Boone County Fairgrounds in Columbia, Missouri. In addition to the annual County Fair, the Fairgrounds hosts many other year-round events. It is also the site of a major RV facility and sits adjacent to a developing 80 acre baseball park. Two of ten proposed diamonds are already open there. Create a free website. Start your own free website.
Arcadia, CA : Home
Watch City Council Meetings. Mayor Pro Tem Peter Amundson. Council Member Roger Chandler. Council Member Sho Tay. Council Member April Verlato. City Mission Statement And Goals. Contact City Hall- Arcadia Advocacy. How Do Cities Work? Request City Council Recognition. Recreation and Community Services. Federal, State and Local Elected Officials. Building Permit and Inspection. Overnight Parking Permit- annual. Overnight Parking Permit- temporary. Get more information about. Contesting a Parking Citation.
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