demo bam file Ion Torrent 314 chip of E. coli 400 bp run for download

BAM file of B22-730 (314v2 E. coli 400 bp run)
Ion Torrent PGM 314v2 run with a mode read length of 400bp and per-base raw read accuracy >99%.

https://s3.amazonaws.com/ion-torrent/pgm/B22-730/B22-730.bam

Source: https://apps.thermofisher.com/apps/publiclib/#/datasets

Creating filtered fastq files of ONLY mapped reads from a BAM file

Filtering BAM files for mapped or unmapped reads

To get the unmapped reads from a bam file use :

samtools view -f 4 file.bam > unmapped.sam, the output will be in sam

to get the output in bam use : samtools view -b -f 4 file.bam > unmapped.bam

To get only the mapped reads use the parameter 'F', which works like -v of grep and skips the alignments for a specific flag.

samtools view -b -F 4 file.bam > mapped.bam

Source: https://www.biostars.org/p/56246/ Sukhdeep Singh

To do this as efficiently as possible, using BBTools:

reformat.sh in=reads.sam out=mapped.fq mappedonly

Also, BBMap has a lot of options designed for filtering, so it can output in fastq format and separate mapped from unmapped reads, preventing the creation of intermediate sam files.  This approach also keeps pairs together, which is not very easy using samtools for filtering.

bbmap.sh ref=reference.fa in=reads.fq outm=mapped.fq outu=unmapped.fq

Source: https://www.biostars.org/p/127992/ Brian Bushnell

Control a fleet of embedded unix systems (eg Raspberry Pi, Orange Pi) using saltstack

HAHAHA I share the same name as a software project. Bizarre discovery today

https://github.com/unixbigot/kevin
Control a fleet of embedded unix systems (eg Raspberry Pi, Orange Pi) using saltstack

github-based, community-maintained list of cancer clinical informatics resources

Sean Davis created a github-based, community-maintained list of cancer clinical informatics resources. 
"Contributions are welcome!" https://lnkd.in/d-uphUc

For now, it's named as

ci4cc-informatics-resources 

https://github.com/seandavi/ci4cc-informatics-resources

offline plotly Gantt plots using Python/pandas

modified from https://plot.ly/python/gantt/#use-a-pandas-dataframe to do offline and outside of ipython

Verily (Google) is hiring Computational Biologists

https://www.google.com/about/careers/search?src=Online/Job+Board/indeed#!t=jo&jid=228815001&

the role is described as 'hardware engineering' interestingly. the preferred qualifications are very loose...

• Demonstrated knowledge of core concepts in machine learning or probability and statistics.
• Willingness to learn molecular and cell biology, computer science, and statistics.
• Demonstrated effective written and verbal communication skills.

I bet they will be inundated with submissions! 

Put your application in! 

Compiling BWA on Ubuntu 16.04.1 LTS

#install prereq else you will get utils.c:33:18: fatal error: zlib.h: No such file or directory
sudo apt-get install zlib1g-dev

#download the latest version and compile
$ wget http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.12.tar.bz2
$ tar jxvf bwa-0.7.12.tar.bz2
$ cd bwa-0.7.12/
$ make