BOL: All wire posts

Wire post by BioStar

BioStar — Mon, 09 Dec 2019 07:54:44 -0600

So you want to be a computational biologist? https://www.nature.com/articles/nbt.2740 #computational_biology #bioinformatics

Wire post by Jit

Jit — Sat, 07 Dec 2019 20:33:54 -0600

https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources/blob/master/Next%20Generation%20Sequencing%20spreadsheet%20-%20T.tsv #NGS #CheatSheet

Wire post by Jit

Jit — Thu, 05 Dec 2019 05:50:39 -0600

#BlobToolKit can be used during #assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. https://blobtoolkit.genomehubs.org/view #Genome #Blob #Con

Wire post by Jit

Jit — Mon, 02 Dec 2019 08:46:31 -0600

Perl script to run in parallel https://perlmaven.com/speed-up-calculation-by-running-in-parallel #Perl #Parallel #Script #Core #Thread

Wire post by Neel

Neel — Fri, 29 Nov 2019 22:14:54 -0600

Perl onliner to add string to each of the fasta header. $ perl -p -e 's/^(>.*)$/$1-origin/g' in.fasta > out.fasta #String #Header #Fasta

Wire post by Neel

Neel — Mon, 25 Nov 2019 22:26:37 -0600

Multifasta 2 singlefasta cat toy.fasta| awk '{ if (substr($0, 1, 1)==">" {filename=(substr($0,2) ".fa")} print $0 > filename }' #Split #fasta #multifasta

Wire post by LEGE

LEGE — Mon, 25 Nov 2019 13:37:35 -0600

One can evaluate the accuracy of a mapper or a SNP caller with wgsim_eval.pl
that comes with the package. #Evaluate #Mapping #SNP

Wire post by LEGE

LEGE — Mon, 25 Nov 2019 12:13:22 -0600

Deep_learning course https://www.slideshare.net/TessFerrandez/notes-from-coursera-deep-learning-courses-by-andrew-ng #AI #DeepLearn

Wire post by LEGE

LEGE — Mon, 25 Nov 2019 12:02:37 -0600

Multiline to singleline covert. $ awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input.fa #Multi #Single #Convert #awk

Wire post by LEGE

LEGE — Mon, 25 Nov 2019 09:23:51 -0600

#Estimate the #insert #size with mapped reads $ head -10000 mappings.sam | awk '{ if ($9 > 0) { N+=1; S+=$9; S2+=$9*$9 }} END { M=S/N; print "n="N", mean="M", stdev="sqrt ((S2-M*M*N)/(N-1))}'

Wire post by Rahul Nayak

Rahul Nayak — Sun, 24 Nov 2019 20:28:53 -0600

Graph reference genome https://vimeo.com/184983995 #Graph #Reference #Genome #GraphRef

Wire post by Jit

Jit — Thu, 21 Nov 2019 22:59:14 -0600

This works and I dont know how :) perl -pe '}{$_=$.' filename #Perl #Magic #PerlMagic

Wire post by Rahul Nayak

Rahul Nayak — Sat, 16 Nov 2019 12:03:10 -0600

https://www.frontiersin.org/articles/10.3389/fmicb.2018.00973/full #Recent #HGT

Wire post by Neel

Neel — Sat, 16 Nov 2019 02:35:17 -0600

Kill the screen $ screen -X -S [session # you want to kill] quit #Screen #Quit #Linux #Session #Remote

Wire post by Neel

Neel — Fri, 15 Nov 2019 23:13:24 -0600

#Rename the #fasta #header and #keep first $ perl -ne 'if (/^(>\S+)/){print "$1\n";}else{print $_;}' realTestDATA.fa > realTestDATA_headerCorrected.fa #Perl