BOL: Wire posts tagged with 'Fasta'

Wire post by Rahul Nayak

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

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 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 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 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 Poonam Mahapatra

Poonam Mahapatra — Tue, 15 May 2018 09:46:57 -0500

Convert fasta to 2bit $ faToTwoBit myAssembly.fa myAssembly.2bit #Fasta #2bit #Convert

Wire post by Manisha Mishra

Manisha Mishra — Tue, 17 Apr 2018 17:43:19 -0500

Remove the sequence by fasta ids. awk 'BEGIN{while((getline<"ids.txt")>0)l[">"$1]=1}/^>/{f=!l[$1]}f' seq.fa #Remove #Delete #ids #fasta

Wire post by Manisha Mishra

Manisha Mishra — Tue, 17 Apr 2018 16:37:42 -0500

Extract fasta with Ids. $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #extract #fasta #sequence #ids

Wire post by Jit

Jit — Mon, 09 Apr 2018 04:20:46 -0500

Convert lowercase letter to N:$ sed -e '/^>/! s/[[:lower:]]/N/g' in.fasta > out.fasta #Convert #Lowercase #Fasta #N

Wire post by Rahul Nayak

Rahul Nayak — Fri, 23 Mar 2018 10:18:22 -0500

#Convert #fasta file to uppercase/lowercase, without altering the annotation line $ awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' name.fasta

Wire post by Jit

Jit — Mon, 12 Feb 2018 05:57:42 -0600

#GFA to #Fasta file conversion. $ grep '^S' example.gfa |awk '{print ">"$2; print $3}' > example.fa

Wire post by Jit

Jit — Mon, 05 Feb 2018 07:42:32 -0600

#GFA to #FASTA file conversion. awk '/^S/{print ">"$2"\n"$3}' in.gfa | fold > out.fa

Wire post by Jit

Jit — Thu, 14 Dec 2017 04:00:38 -0600

awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} {if ($2) print ">"$0}' all_p_ctg.fa > all_p_ctg_CORRECTED.fa #remove #empty #clean #fasta

Wire post by Poonam Mahapatra

Poonam Mahapatra — Mon, 11 Dec 2017 04:22:59 -0600

Remove duplicate fasta ids: awk '/^>/{f=!d[$1];d[$1]=1}f' in.fa > out.fa #duplicate #fasta #ids

Wire post by Surabhi Chaudhary

Surabhi Chaudhary — Sun, 03 Dec 2017 17:47:00 -0600

Remove the unwanted characters from Fasta file: sed -e '/^[^>]/s/[^ATGCatgc]/N/g' infile.fa #sed #unwanted #illegal #remove #correct #fasta #linux