BOL: Rahul Nayak's wire posts

Wire post by Rahul Nayak

Rahul Nayak — Thu, 20 Dec 2018 13:18:03 -0600

Add number in fasta header $ awk '/^>/{$0=$0"_"(++i)}1' infile.fa #fasta #header #add #number #count

Rahul Nayak — Fri, 14 Dec 2018 03:38:55 -0600

sudo find /tmp -type f -atime +10 -delete #Delete all tmp files created within 10 days #Linux

Rahul Nayak — Thu, 13 Dec 2018 09:00:58 -0600

#Search a #genome sequence for secondary #metabolite biosynthetic gene clusters https://antismash.secondarymetabolites.org/#!/start

Rahul Nayak — Wed, 21 Nov 2018 14:12:31 -0600

Bioinformatics faculty jobs at https://www.vu.nl/en/employment/vacancies/2018/18405ASSISTANTPROFESSORBIOINFORMATICS.aspx #Bioinformatics #Jobs

Rahul Nayak — Wed, 14 Nov 2018 17:33:48 -0600

> pchisq(15, df=2, lower.tail=FALSE); [1] 0.0005530844 #Chi-square #R #P-value

Rahul Nayak — Tue, 06 Nov 2018 06:52:38 -0600

Long reads: their purpose and place https://academic.oup.com/hmg/article/27/R2/R234/4996216 #Long #reads #informations

Rahul Nayak — Thu, 25 Oct 2018 08:33:59 -0500

Variant calling workflow http://www.htslib.org/workflow/ #Variant #Calling #Tutorial

Rahul Nayak — Thu, 25 Oct 2018 05:06:51 -0500

AB1 file format http://www6.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf #AB1 #File #Format

Rahul Nayak — Mon, 08 Oct 2018 08:42:39 -0500

https://www.ebi.ac.uk/about/news/announcements/25-genomes-UK-species #Genomes #Sequenced #UK

Rahul Nayak — Mon, 08 Oct 2018 04:07:37 -0500

https://pb-falcon.readthedocs.io/en/latest/quick_start.html#quick-start #Falcon-Unzip #Genome #Assembly

Rahul Nayak — Sun, 07 Oct 2018 11:03:59 -0500

https://blog.rstudio.com/2018/10/05/r2d3-r-interface-to-d3-visualizations/ #r2d3 #visualization

Rahul Nayak — Thu, 04 Oct 2018 16:09:46 -0500

Mapping subreads https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf #R

Rahul Nayak — Sat, 22 Sep 2018 18:44:09 -0500

Nice genome assembly tutorial http://aidenlab.org/assembly/manual_180322.pdf #Assembly #Tutorial #Genome #NGS

Rahul Nayak — Wed, 05 Sep 2018 05:09:15 -0500

Multi-line fasta to single line fasta $ perl -pe '/^>/ ? print "\n" : chomp' in.fasta | tail -n +2 > out.fasta #Multiline #Singleline #Fasta

Rahul Nayak — Tue, 04 Sep 2018 09:18:39 -0500

Snakemake install Ubuntu $ sudo apt-get install snakemake #snakemake #Ubuntu #Install