Monthly Archives: August 2011

Email from Ryan I’ve moved a preliminary copy of that data to the TopStrandFiles folder: ls /nfs/sva01/SequenceAnalyses/TopStrandFiles/top_strand_cumulative_* -lh -rwxrwxrwx 1 solexa goldsteinlab 15K Jul 20 17:05 /nfs/sva01/SequenceAnalyses/TopStrandFiles/top_strand_cumulative_exome__7.20.11.txt -rwxrwxrwx 1 solexa goldsteinlab 13K Jul 20 17:05 /nfs/sva01/SequenceAnalyses/TopStrandFiles/top_strand_cumulative_genome__7.20.11.txt Hope this helps, it … Continue reading →

Currently, we are updating the pipeline to support human genome build37, detail refers to bioinformatic wiki As of today: Aug. 23rd, 2011, I have got both bwa59_b37_v1 and bwa59_b37_v4 running. The major difference between these two are the samtools version. … Continue reading →

Part I: getting B37 topstrand file converted 1. calling a script to update run summary file and create B37 topstrand if not yet created. 1. Script: /home/jl407/svnroot/bioinfoDev/jyli/topStrandRelated/modRunSmry.pl 2. Input (run_summary file owned by Ryan) i.e. exRealign_Summary_09.30.11.txt 3. Input log file: … Continue reading →

Email 1 from Jessica: Hi Jianying and Hee Shin, Here are my day to day tasks which will be passed on to both of you while I’m on maternity leave: * Hee Shin will be in charge of SVA project … Continue reading →

Hi Jianying, Before staring the re-alignment effort full force, I would let David and SVA users know that besides a new reference sequence, there will be a Samtools upgrade. Here are some easy checks I would recommend. (A) Comparison to … Continue reading →

Currently: /sample/Script/coverage.sh is called to fire up /nfs/chgv/seqpipe01/SOFTWARE/alignment_scripts/average_coverage.pl $script_dir/average_coverage.pl $pileup_file > $coverage_file Now, Step 1. Copy “average_coverage.pl” to lsrc svnroot Step 2. Modify “average_coverage.pl” to take in vcf format Step 3.

Here is the email from Joe, who did for Hee Shin following the documentation he did for me earlier. I need this for customized library: Hee Shin, Jianying and I ran into a problem in the past in term of … Continue reading →

Email from Jessica Hi Jianying, For the 65kit, I did not modify the build 19 file before I lifted over coordinates. Here’s the script I used to lift over the coordinates from build 19 to build 18 for the 65kit: … Continue reading →

Let’s change the index ONLY and to see how complex it can get. To-do list 1. coverage computation: samtools vs. bcftools 2. concordance check R script 3. copy drive parameter for HK Test run on exome sample Email from Ryan … Continue reading →

In order to compute the overall and exonic coverage, we need the exonic coordinate for human genome build 37 Advice from Dongliang Hi Jianying, To generate this file I will need a clean SVA project aligned and called in build … Continue reading →