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Oil change To purchase kit, here are links to OEM but much cheaper than dealership http://www.e90post.com/forums/showthread.php?t=485071 I usually buy all my filters from germanfilters.com, but i came across Tischer, and it lists OEM filters for $9 if I buy the … Continue reading →

I replaced the battery, then it stalls after starts. It turns out that the vehicle needs to relearn ECU. To clean the throttle body, I found a very good youtube link. How to change the CV boots How to change … Continue reading →

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Get VEP files downloaded VEP A list of all available download from Ensembl [jl407@sva .vep]$ wget -r ftp://ftp.ensembl.org/pub/release-65/variation/VEP/homo_sapiens/ homo_sapiens_vep_65.tar.gz

Using b57mod018 as an example: From the scripts generating at: 12/22/2011 at 15:00 p.m.. Here are the timing for those files that generated: [jl407@login-05 b57mod018]$ ls -tral Run1/*.fastq -rw-r–r– 1 jl407 chavi 58803117922 Dec 22 19:31 Run1/s.1.1.maq.fastq -rw-r–r– 1 jl407 … Continue reading →

With the implementation of GATK for variant call, it was suggested as “better practice” by Broad Institute to include “base calling score recalibration”. Here is what has been done in the past Getting the set up for both dscr and … Continue reading →

Two major annotation package available to test are Annovar and Ensembl’s VEP Need to test/compare which one is suitable for us Kick-off meeting on 01/09/2012, Download EVS database at NHLBI web portal The following downloadable files contain SNPs and coverage … Continue reading →

perl /nfs/chgv/seqpipe01/SOFTWARE/alignment_scripts/sample_info_meta.pl /nfs/chgv/seqpipe01/WGseqCassava18/list_in_retro /nfs/chgv/seqraw01/summaries/wgRun_Summary_v1.8_b37__11.29.11.txt /nfs/chgv/seqpipe01/ALIGNMENT/sample_info perl /nfs/chgv/seqpipe01/SOFTWARE/alignment_scripts/submit_sample_jobs_meta.pl /nfs/chgv/seqpipe01/WGseqCassava18/list_in_retro genome 0 seqpipe01 bwa seqsata13 all high jl407 batch 1 compute2.lsrc.duke.edu perl /nfs/chgv/seqpipe01/SOFTWARE/alignment_scripts/submit_sample_jobs_meta.pl /nfs/chgv/seqpipe01/WGseqCassava18/list_in_retro genome 0 seqpipe01 all

How to check the eqw status: qstat -j job_ID -explain E

Status: b57mod008 –> need re-run b57mod010 –> need re-run b57mod011 –> test ad hoc run, done and bam file copied b57mod016 –> test ad hoc run, done and bam file copied b57mod030 –> copying, done and bam file copied b57mod013 … Continue reading →