BOL: Wire posts tagged with 'Convert'

Wire post by Jit

Jit — Fri, 20 Aug 2021 10:35:30 -0500

#Convert #FASTQ to FASTA and set bases of #quality lower than 20 to N $ seqtk seq -aQ64 -q20 -n N IN.fastq > OUT.fasta

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 Jit

Jit — Mon, 28 Jan 2019 04:58:01 -0600

for i in $(ls *.ab1); do convert_trace -out_format scf < $i > ${i%.ab1*}.scf; done #Convert #AB12SCF #SCF #AB1

Wire post by Neel

Neel — Sun, 27 Jan 2019 14:56:30 -0600

(smrttools) ➜ allBam for i in *.bam; do bamtools convert -format fasta -in $i -out $i.fasta; done #Convert #fasta

Wire post by Jit

Jit — Mon, 22 Oct 2018 09:17:39 -0500

Tab file to FASTA file $ awk '{print ">"$1"\n"$2}' allSeq_tm.txt > allSeq_tm.fa #Fasta #Tab #Convert #Tab2Fasta

Wire post by Neel

Neel — Thu, 18 Oct 2018 09:00:03 -0500

BAM2BED conversion bamToBed -i overall_exp_genome_rep1.bam > alignment.bed #Bed #bam #bamToBed #convert

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 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 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

Wire post by Poonam Mahapatra

Poonam Mahapatra — Tue, 15 May 2018 09:48:05 -0500

Convert 2bit to psl $ blat myAssembly.2bit -oneOff=0 -noHead myQueryContigSeqs.fa myHits.psl #Convert #psl #2bit #blat

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 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 — Thu, 23 Nov 2017 08:23:41 -0600

Fastq 2 fasta. $ sed -n '1~4s/^@/>/p;2~4p' test.fastq > test.fasta #fastq #fasta #convert