http://www.youtube.com/watch?v=Wf_a6xtCVpo

Source: Welcome to the Bioinformatics Capstone – YouTube

An in-depth article that explains how a relational database handles an SQL query and the basic components inside a database.

Source: How does a relational database work – Coding Geek

If you follow the headlines, your confidence in science may have taken a hit lately.

Peer review? More like self-review. An investigation in November uncovered a scam in which researchers were rubber-stamping their own work, circumventing peer review at five high-profile publishers.

Scientific journals? Not exactly a badge of legitimacy, given that the International Journal of Advanced Computer Technology recently accepted for publication a paper titled “Get Me Off Your Fucking Mailing List,” whose text was nothing more than those seven words, repeated over and over for 10 pages. Two other journals allowed an engineer posing as Maggie Simpson and Edna Krabappel to publish a paper, “Fuzzy, Homogeneous Configurations.”

 

Source: Science Isn’t Broken | FiveThirtyEight

Legions of programmers now stream their work on Livecoding.tv, a site that turns their lonely labor into something more …

Source: The Strange Appeal of Watching Coders Code — Backchannel — Medium

Plugin-free, realtime communication of video, audio and data using WebRTC.

Source: Getting Started with WebRTC – HTML5 Rocks

##### ERROR MESSAGE: SAM/BAM/CRAM file /media/raony/storage/received_exomes/020715/VSS.bam is malformed: Invalid file pointer: 1091655611930580
INFO 09:09:08,041 SAMDataSource$SAMReaders – Done initializing BAM readers: total time 2.47
INFO 09:09:09,790 IntervalUtils – Processing 46347343 bp from intervals
INFO 09:09:10,005 GenomeAnalysisEngine – Preparing for traversal over 14 BAM files
INFO 09:09:10,913 GenomeAnalysisEngine – Done preparing for traversal
INFO 09:09:10,913 ProgressMeter – [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 09:09:10,914 ProgressMeter – | processed | time | per 1M | | total | remaining
INFO 09:09:10,914 ProgressMeter – Location | sites | elapsed | sites | completed | runtime | runtime
INFO 09:09:10,914 DepthOfCoverage – Per-Locus Depth of Coverage output was omitted
INFO 09:09:40,917 ProgressMeter – chr1:949759 90012.0 30.0 s 5.6 m 0.0% 27.5 h 27.5 h

Google Drive

Source: What does it take to make Google work at scale? – Google Slides

@RG     ID:D07MJ        PL:IONTORRENT   PU:PGM/900

WARNINGS

/media/raony/storage/received_exomes/5exomes/R_2014_03_14_12_01_11_user_PR6-64-KLF_Auto_user_PR6-64-KLF_90.bam
TAMANHO:54.6GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/5exomes/R_2014_03_14_12_01_11_user_PR6-64-KLF_Auto_user_PR6-64-KLF_90.bam.bai
ID:8TB8O
/media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_29_40_user_PR1-7-ACLF_Auto_user_PR1-7-ACLF_134.bam
TAMANHO:35.3GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_29_40_user_PR1-7-ACLF_Auto_user_PR1-7-ACLF_134.bam.bai
ID:R44KW
/media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_30_52_user_PR2-93-LGLF_Auto_user_PR2-93-LGLF_124.bam
TAMANHO:43.1GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_30_52_user_PR2-93-LGLF_Auto_user_PR2-93-LGLF_124.bam.bai
/media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_31_20_user_PR3-92-LEGF_Auto_user_PR3-92-LEGF_126.bam
TAMANHO:43.4GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_31_20_user_PR3-92-LEGF_Auto_user_PR3-92-LEGF_126.bam.bai
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/june_july_2014/MM140545/coverage_analysis_out/IonXpress_008_R_2014_06_10_15_13_57_user_PR3-131-SP_MM140545_CM_AT-1_Auto_user_PR3-131-SP_MM140545_CM_AT-1_166.bam.bai

/media/raony/storage/received_exomes/020715/Arquivos da Natália/VSS.bam
TAMANHO:15.5GiB
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/020715/Arquivos da Natália/VSS.bai
ID:Q3ESQ.IonXpress_013
achou ampliseq
/media/raony/storage/received_exomes/020715/Arquivos da Natália/TYSS.bam
TAMANHO:21.1GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/020715/Arquivos da Natália/TYSS.bai
ID:RV1P2.IonXpress_012
achou ampliseq
/media/raony/storage/received_exomes/020715/Arquivos da Natália/JPBS.bam
TAMANHO:21.4GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/020715/Arquivos da Natália/JPBS.bai
ID:A7H2K.IonXpress_006
achou ampliseq
/media/raony/storage/received_exomes/020715/Arquivos da Natália/TRS.bam
TAMANHO:21.3GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/020715/Arquivos da Natália/TRS.bai
ID:RV1P2.IonXpress_011

/media/raony/storage/received_exomes/vcfmms2/PR2-40-mm13490.bam
TAMANHO:30.9GiB
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/vcfmms2/PR2-40-mm13490.bam.bai
ID:ND13A

/media/raony/storage/received_exomes/150515/MM150125MO.bam
TAMANHO:23.9GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/150515/MM150125MO.bam.bai
ID:QGLE1.IonXpress_015
achou ampliseq
/media/raony/storage/received_exomes/150515/MM150137LN.bam
TAMANHO:28.0GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/150515/MM150137LN.bam.bai
ID:QGLE1.IonXpress_016

/media/raony/storage/received_exomes/exomes070513/PR4-11-mm13174_13.bam
TAMANHO:31.1GiB
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
ID:IXZYA

cat human_g1k_v37.fasta | sed ‘s/>/>chr/g’ > human_g1k_v37chr.fasta

http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference
java -Xmx40g -jar /home/raony/bin/gatk/GenomeAnalysisTK.jar -T DepthOfCoverage -I ampliseq.group2.list -L /home/raony/datasets/beds/AmpliSeqExome.20141113.designed_effective.bed -R /home/raony/datasets/b37/human_g1k_v37chr.fasta -dt BY_SAMPLE -dcov 5000 -l INFO –omitDepthOutputAtEachBase –omitLocusTable –minBaseQuality 0 –minMappingQuality 20 –start 1 –stop 5000 –nBins 200 –includeRefNSites –countType COUNT_FRAGMENTS -o group2.DATA
java -Xmx40g -jar /home/raony/bin/gatk/GenomeAnalysisTK.jar -T DepthOfCoverage -I ampliseq.group3.list -L /home/raony/datasets/beds/AmpliSeqExome.20141113.designed_effective.bed -R /home/raony/datasets/b37/human_g1k_v37chr.fasta -dt BY_SAMPLE -dcov 5000 -l INFO –omitDepthOutputAtEachBase –omitLocusTable –minBaseQuality 0 –minMappingQuality 20 –start 1 –stop 5000 –nBins 200 –includeRefNSites –countType COUNT_FRAGMENTS -o group3.DATA

A smorgasbord of various slides on metagenome assembly, presented at the 2015 BEACON congress.

Source: 2015 beacon-metagenome-tutorial

Perl hackers have now, as of today the 16th August 2015, been uploading Perl modules ontoCPAN via PAUSE for 20 years. Andreas König, who did that first upload, is still releasing to CPAN, and as I write this his most recent upload is the same module that was first released to CPAN.
Source: CPAN is 20! | NeilB [blogs.perl.org]