BOL: All wire posts

Wire post by Neel

Neel — Mon, 01 Oct 2018 11:59:41 -0500

GATK is open source https://software.broadinstitute.org/gatk/ #GATK #Broad

Wire post by Neel

Neel — Mon, 01 Oct 2018 11:41:35 -0500

Reverse complement of fasta sequence $ tr -d "\n " < chrII.fa | tr "[ATGCatgcNn]" "[TACGtacgNn]" | rev > chrII_reverseHai.fa #Reverse #Complement #DNA

Wire post by Neel

Neel — Mon, 01 Oct 2018 09:55:38 -0500

Add some text at the beginning of the file $ echo -e "chrII_reverse\n$(cat chrII_reverse.fa )" > chrII_reverse.fa #Add #FirstLine #Text

Wire post by Neel

Neel — Mon, 01 Oct 2018 09:03:12 -0500

Multifasta to singleline fasta. $ awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa #Multi #Single #Fasta #Convert

Wire post by BioStar

BioStar — Wed, 26 Sep 2018 05:50:30 -0500

Split the fasta $ pyfasta split -k 100 -o 20 input.fasta -n 1 #split #pyfasta #overlaps

Wire post by Rahul Nayak

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

Wire post by BioStar

BioStar — Sat, 22 Sep 2018 07:03:57 -0500

Remove empty line from fasta. $ sed -i '/^$/d' standard_output.final.scaffolds_online.fasta #Empty #Fasta #Remove

Wire post by BioStar

BioStar — Sat, 22 Sep 2018 06:44:28 -0500

MultiLine fasta to oneline fasta converter awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa #Multiline #Oneline

Wire post by BioStar

BioStar — Fri, 21 Sep 2018 10:21:12 -0500

Understanding Paired End and Mate pair reads http://www.biorigami.com/wp-content/uploads/2012/02/PAIREDEND-MATEPAIR.pdf #Reads #Mate #Pairs #PE #Reads #MatePair

Wire post by Jit

Jit — Wed, 19 Sep 2018 05:43:56 -0500

http://loupe.10xgenomics.com #10XGenomics #10X #Phase #Haplotype #View

Wire post by Jit

Jit — Fri, 14 Sep 2018 04:05:53 -0500

Genome Assembly Cookbook http://aidenlab.org/assembly/manual_180322.pdf #HiC #3D-DNA #Juicer

Wire post by BioStar

BioStar — Sun, 09 Sep 2018 16:37:10 -0500

https://github.com/Ensembl/ensembl-vep #Variant #Effect #Predictor #Github

Wire post by BioStar

BioStar — Sun, 09 Sep 2018 16:10:50 -0500

Variant Effect Predictor http://www.ensembl.org/Tools/VEP #Variant #Effect #Predictor

Wire post by Abhimanyu Singh

Abhimanyu Singh — Thu, 06 Sep 2018 16:33:41 -0500

Efficiency of #PacBio long read #correction by 2nd generation #Illumina sequencing https://www.sciencedirect.com/science/article/pii/S0888754317301660

Wire post by BioStar

BioStar — Wed, 05 Sep 2018 10:52:26 -0500

#Nigerian Society for #Bioinformatics and Computational Biology (#NISBCB) http://cubre.covenantuniversity.edu.ng/index.php/nigeria-society-for-bioinformatics-and-computatational-biology-nisbcb/#.W4_7m