LoveRainbow

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 10 pack vs germanfilters which was something like 10.87.

Before I submit an order, is $9/filter the cheapest I’ll find or does someone know of a cheaper source?

Thanks.

http://www.trademotion.com/partlocat…egoryID=104047

Item Number UOM Qty MSRP Price
11427566327_10Pack Each $124.60 $124.60
$90.00
BMW E90/91/92 OEM Oil Filter 10 Pack
10 pack of OEM E90/91/92 oil filters at a great price! Price includes FREE GROUND SHIPPING!!!

To reset the meter, I found a useful link.

	
Step 1: At ignition OFF (POS 0) position

	
Step 2: Press and Hold the trip odometer button while turning key to position 1 (ACCESSORY)

	
Step 3: Keep the button depressed (about 5 secs.) until you see "Oil Service" or "Inspection" with "Reset" or "Re" in the display

	
*Note: On vehicles with "High" cluster, you will also see the amount of fuel (in litres) remaining until next service

	
Step 4: Press the button again and hold for approx. 5 secs. until "Reset" or "Re" flashes

	
Step 5: While the display is flashing, briefly press the button again to reset the Service Interval. After the display has shown the new interval you should see "END SIA" for about 2 secs.

	
Note that if the "Reset" or "Re" does not flash, then you have not met the minimum consumption level and cannot reset.

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 the timing belttiming belt. Also at Scotty Kilamer for details

To replace valve cover gasket seal, youtube link.

A car cranks but fails to start, check this out.

What if the starter fails? Here are some tricks. I like it and recommend Scotty Kilmer

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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 chavi 58803117922 Dec 22 22:44 Run1/s.1.2.maq.fastq
-rw-r–r– 1 jl407 chavi 59684349150 Dec 23 00:32 Run1/s.2.1.maq.fastq
-rw-r–r– 1 jl407 chavi 59684349150 Dec 23 01:33 Run1/s.2.2.maq.fastq
-rw-r–r– 1 jl407 chavi 58910000237 Dec 23 02:16 Run1/s.3.1.maq.fastq
-rw-r–r– 1 jl407 chavi 58910000237 Dec 23 03:11 Run1/s.3.2.maq.fastq
[jl407@login-05 b57mod018]$ ls -tral Run1/*.sam
-rw-r–r– 1 jl407 chavi 161606690649 Dec 27 07:04 Run1/s.3.sam
-rw-r–r– 1 jl407 chavi 163696435930 Dec 27 07:10 Run1/s.2.sam
-rw-r–r– 1 jl407 chavi 160301999828 Dec 27 07:43 Run1/s.1.sam
[jl407@login-05 b57mod018]$ ls -tral Run1/sorted*
-rw-r–r– 1 jl407 chavi 40203860916 Dec 27 15:05 Run1/sorted.Run1.3.bam
-rw-r–r– 1 jl407 chavi 40927775265 Dec 27 15:29 Run1/sorted.Run1.2.bam
-rw-r–r– 1 jl407 chavi 41483829940 Dec 27 15:35 Run1/sorted.Run1.1.bam
[jl407@login-05 b57mod018]$ ls -al com
ls: com: No such file or directory
[jl407@login-05 b57mod018]$ ls -al combined/
total 232530888
drwxr-xr-x 2 jl407 chavi 4096 Dec 29 04:00 .
drwxr-xr-x 6 jl407 chavi 4096 Dec 22 15:10 ..
-rw-r–r– 1 jl407 chavi 870 Dec 29 04:00 average_coverage.txt
-rw-r–r– 1 jl407 chavi 120898509151 Dec 27 23:32 combined.bam
-rw-r–r– 1 jl407 chavi 116270527895 Dec 28 15:50 combined_rmdup.bam
-rw-r–r– 1 jl407 chavi 8777072 Dec 28 23:09 combined_rmdup.bam.bai
-rw-r–r– 1 jl407 chavi 1901 Dec 28 22:33 metrics_alignment
-rw-r–r– 1 jl407 chavi 2506 Dec 28 15:50 metrics_duplicates
-rw-r–r– 1 jl407 chavi 159 Dec 22 15:10 rg.txt

Summary:

1. Occupies 1.3 TB (intermediate files 1.1TB)
2. mergeFastq step: 4 – 12 hours
3. ALN: 30 – 48 hours
4. SAMPE: 8 – 15 hours
5. SAM/BAM file processing (conversion and sort): 8 hours
6. MergeBam: 8 hours
7. Remove duplicate:16 hours
8. Indexing bam: 16 hours

Total disk usage: 1.3 TB
Total processing time: 3 – 4.5 days

Copying back to lsrc took very short time, 1 – 2 hours

[jl407@sva b57mod018]$ ls -al combined/
total 114001116
drwxr-sr-x 2 jl407 sequencing 4096 Jan 3 08:42 .
drwxr-sr-x 5 jl407 sequencing 4096 Dec 29 06:04 ..
-rw-r–r– 1 jl407 sequencing 870 Dec 29 04:00 average_coverage.txt
-rw-r–r– 1 jl407 sequencing 116270527895 Dec 28 15:50 combined_rmdup.bam
-rw-r–r– 1 jl407 sequencing 8777072 Dec 28 23:09 combined_rmdup.bam.bai
-rw-r–r– 1 jl407 sequencing 1901 Dec 28 22:33 metrics_alignment
-rw-r–r– 1 jl407 sequencing 2506 Dec 28 15:50 metrics_duplicates
-rw-r–r– 1 jl407 sequencing 159 Jan 3 08:42 rg.txt

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 lsrc.

At dscr

1. Script: /home/chavi/jl407/GATK-testing/workingDir/GATK_recal.pl & /home/chavi/jl407/GATK-testing/workingDir/Global.pm
2. Sample command:
qsub /home/chavi/jl407/GATK-testing/workingDir/GATK_recal.pl
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/combined/combined_rmdup.bam
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/GATK/b57mod030_precal.csv
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/combined/combined_recal.bam
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/GATK/b57mod030_recal.csv
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/GATK/
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/GATK/

At lsrc

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 data for the ESP 5400 exomes (chromosomes 1-22, and X).
ESP5400.snps.txt.tar.gz (SNPs and annotations in space-delimited text format)
ESP5400.snps.vcf.tar.gz (SNPs and annotations in VCF format – same data as ESP5400.snps.txt.gz)
ESP5400.coverage.all_sites.txt.tar.gz (sequencing coverage data for every sites in our targets)
ESP5400.coverage.seq_blocks.txt.tar.gz (sequencing coverage summary data for every squencing block in our targets)

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 –> old run not finished yet, ad hoc run,
b57mod018 –> testing new run with RG, done and bam file copied
b57mod020
b57mod021
b57mod022 –> testing new run with RG, done and bam file copied