BOL

Assembly Conversion https://ics.hutton.ac.uk/tablet/assembly-conversion/ #Assembly #Conversion #NGS

Machine learning https://www.r-bloggers.com/explaining-black-box-machine-learning-models-code-part-1-tabular-data-caret-iml/amp/ #machinelearning #machine

https://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it #VCF #vcf #SNP

sort -k2 -n genome.fa #Sort #Column2 #Bash

Useful #tools for #genome analysis https://gigascience.biomedcentral.com/articles/10.1186/s13742-015-0077-2

#Install #BioPython $ python2.7 -m pip install biopython $ python3.6 -m pip install biopython $ pypy -m pip install biopython

http://qb.cshl.edu/assemblytics/ #Analysis #Genome #Mummer #Assembly #Assemblytics

https://www.r-bloggers.com/a-comparative-review-of-the-r-commander-gui-for-r/amp/ #R #GUI

Replace lowercase to N. perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna #Mask #Lowecase2N #LowerCase

Unmask lowercase. perl -pe '/^[^>]/ and $_=uc' genomic.fna > genomic.unmasked.fna #LowerCase #Unmask

http://education.knoweng.org/sequenceng/ #learn #ngs

Transcriptome assembly https://www.rna-seqblog.com/tag/transcriptome-assembly/ #RNA-seq #Transcriptome #Assembly

Call for applications : Early Career #Fellowships in #Biomedical #Research https://www.indiaalliance.org/news/239

Get unique ids from column 1 in Linux. $ cat output_file | cut -f 1 | sort | uniq > allUniqOUT #Unique #Linux #Cut

#tBLASTn #command line $ tblastn -query Avaga.pep.out.45.fa -db myDB -outfmt 6 -out output_file -evalue 1e-5 -max_target_seqs 1 #Blast #Protein