BOL: All wire posts

Wire post by Jit

Jit — Thu, 30 Jun 2016 04:48:56 -0500

Extract reference nucleotide from BAM file: samtools view your.bam | awk '{print substr( $10, 100, 1)}' #SAM #BAM #Samtools #Tricks #NGS

Wire post by Poonam Mahapatra

Poonam Mahapatra — Wed, 29 Jun 2016 15:31:47 -0500

#Extract #Chromosome #Number And Start Position #Reads: samtools view bamfile.bam|awk '{print $3 "\t" $4 "\t" $4+length($10)-1}' > newfile.tab

Wire post by Jit

Jit — Mon, 27 Jun 2016 09:02:08 -0500

#NGS basics http://deeptools.readthedocs.io/en/latest/content/help_glossary.html #Tutorial #Help

Wire post by Jit

Jit — Mon, 27 Jun 2016 08:39:50 -0500

Check if BAM file is sorted or not use: for F in `find . -name "*.bam"`; do echo $F; samtools index ${F} ; done #Sort #BAM #Trick

Wire post by Poonam Mahapatra

Poonam Mahapatra — Fri, 24 Jun 2016 09:16:32 -0500

#Extract all #Reads from #BAM file for a #region Chr10:18000-45500 using #samtools: samtools view input.bam "Chr10:18000-45500" > output.bam

Wire post by Jit

Jit — Fri, 24 Jun 2016 08:55:24 -0500

#Network #Visualization in #R #Tutorial http://kateto.net/network-visualization

Wire post by Shruti Paniwala

Shruti Paniwala — Thu, 23 Jun 2016 09:00:18 -0500

#Extract #tabbed info from #BAM file with samtools: samtools view test.bam|awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $4+length($10)-1}' > file.xls

Wire post by Neel

Neel — Fri, 17 Jun 2016 13:35:47 -0500

#Training in High-Throughput #Sequencing: Common #Guidelines to Enable #Material Sharing, Dissemination, and Reusability http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004937

Wire post by Shruti Paniwala

Shruti Paniwala — Wed, 15 Jun 2016 05:18:40 -0500

Grep all the processor in Linux system $ grep "^processor" /proc/cpuinfo | tail -n 1 | awk '{print $3}' #Grep #OS #Linux #Processor

Wire post by Shruti Paniwala

Shruti Paniwala — Wed, 15 Jun 2016 05:16:04 -0500

Update NCBI BLAST database in your local Linux system $ update_blastdb --passive --decompress nr nt #BLAST #Updates #NT #NR #Linux

Wire post by Abhi

Abhi — Wed, 15 Jun 2016 03:46:24 -0500

Bioinformatics studentship and traineeship at http://www.pondiuni.edu.in/sites/default/files/career-bioinformts-Studentship_130616.pdf #PU #India #Studentship

Wire post by Jit

Jit — Fri, 10 Jun 2016 08:11:01 -0500

This is the #repository of the #Genomics Core High Performance Computing for Genomics #workshop. https://github.com/GenomicsCoreLeuven/vsc_ngs_workshop

Wire post by Abhi

Abhi — Thu, 09 Jun 2016 03:27:06 -0500

#Tinker With a #Neural Network Right Here in Your #Browser.
Promise. http://playground.tensorflow.org

Wire post by Jit

Jit — Wed, 08 Jun 2016 19:11:35 -0500

The #bacterial #DnaA-trio #replication origin element specifies single-stranded DNA initiator #binding http://www.nature.com/nature/journal/vaop/ncurrent/full/nature17962.html

Wire post by Jit

Jit — Thu, 02 Jun 2016 10:48:07 -0500

polar histogram: pretty and useful http://www.r-bloggers.com/polar-histogram-pretty-and-useful/ #R #Plot #Histogram