BOL: All wire posts

Wire post by Jit

Jit — Wed, 27 Jun 2018 15:20:29 -0500

#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

Wire post by Jit

Jit — Wed, 27 Jun 2018 14:25:58 -0500

perl -e '$/="\n>"; while (<>) { s/>//g; my ($id, $seq) = split /\n/; print ">$_" if length $seq; }' < all_p_ctg.fasta > all_p_ctg_corrected.fasta #Convert #Fasta #Zero

Wire post by Rahul Nayak

Rahul Nayak — Mon, 25 Jun 2018 08:36:09 -0500

Genome in a Bottle http://jimb.stanford.edu/giab/ #GIAB #Genome

Wire post by Jit

Jit — Sat, 23 Jun 2018 16:13:15 -0500

perl -pe 's/[^AGTC\n]/N/gi unless m/>/;' /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds.fasta > /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds_corrected.fasta #Remove #Non-ATCG

Wire post by Jit

Jit — Fri, 22 Jun 2018 11:56:03 -0500

#Zero coverage regions ~/Tools/bedtools2/bin/bedtools genomecov -ibam PvsH_aln_sorted.bam -bga | awk '$4==0' > ZERO_coverage_regions.txt

Wire post by Aaryan Lokwani

Aaryan Lokwani — Fri, 22 Jun 2018 05:53:37 -0500

Sed illegal charters from fasta. $ sed '/^[^>]/ s/[^AGTC]/N/gi' < seq.fa #fasta #otherthanATGC #replace #sed #Linux #illegal

Wire post by Aaryan Lokwani

Aaryan Lokwani — Fri, 22 Jun 2018 05:16:58 -0500

export PERL5LIB=/home/foobar/code #SetPath #Perl

Wire post by Aaryan Lokwani

Aaryan Lokwani — Fri, 22 Jun 2018 04:41:13 -0500

Count the contigs length in index fasta file with samtools. $ awk '{s+=$2}END{print s}' scaffolds.fasta.fai #Fasta #Index #Length #Count #Size #Samtools

Wire post by Jit

Jit — Fri, 22 Jun 2018 04:27:08 -0500

Genome in a Bottle (GIAB) http://jimb.stanford.edu/giab/ #Genome #Consortium #GIAB

Wire post by Aaryan Lokwani

Aaryan Lokwani — Thu, 21 Jun 2018 08:56:41 -0500

#Scientific #converter https://www.rapidtables.com/convert/number/scientific-notation-converter.html

Wire post by Jit

Jit — Tue, 19 Jun 2018 03:42:48 -0500

Genome Assembly:
#Scaffolding Guided by Related
Genomes https://www.duo.uio.no/bitstream/handle/10852/37431/Furenes_Master.pdf?sequence=1

Wire post by Jit

Jit — Fri, 15 Jun 2018 05:39:51 -0500

To upgrade the perl in Linux $ sudo cpan; cpan[1]> upgrade #Perl #Upgrade #Linux #Ubuntu

Wire post by Jit

Jit — Thu, 14 Jun 2018 08:01:13 -0500

Phased the genome http://pb-falcon.readthedocs.io/en/latest/_downloads/Kingan_DiploidGenome_ECUGM2017_BFX.pdf #Falcon #Unzip #PPT

Wire post by Neel

Neel — Tue, 12 Jun 2018 13:30:49 -0500

#Convert a #multi-line #fasta to a #singleline #fasta $ awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' sample1.fa > sample1_singleline.fa

Wire post by Neel

Neel — Tue, 12 Jun 2018 13:14:13 -0500

sed -i -e '/^+/,/^\@/{/^+/!{/^\@/!d}}; /^+/ d; s/@/>/g' OUTPUT.fastq > out.fa #Convert