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Results for "convert"

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• • Poonam Mahapatra@poonam

  

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

  Tags: Fasta, 2bit, Convert

  2176 days ago

• • Poonam Mahapatra@poonam

  

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

  Tags: Convert, psl, 2bit, blat

  2176 days ago

• • Neelam Jha@neelam

  

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

  Tags: Convert

  2148 days ago

• • Neelam Jha@neelam

  

  #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

  Tags: Convert, multi, fasta, singleline, fasta

  2148 days ago

• • Jit@jit.aber

  

  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

  Tags: Convert, Fasta, Zero

  2133 days ago

• • Jit@jit.aber

  

  Converting a VCF into a FASTA given some reference !

  Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528) This script has been modified by others to convert InDels as well, e.g. this by David Eccles ./vcf2fq.pl -f <input.fasta> <all-site.vcf> ...

  Tags: Convert, VCF, FASTA, reference, genome, assembly, phase

  2110 days ago

• • Neelam Jha@neelam

  

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

  Tags: Multi, Single, Fasta, Convert

  2037 days ago

• • Jit@jit.aber

  

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

  Tags: Fasta, Tab, Convert, Tab2Fasta

  2016 days ago

• • Neelam Jha@neelam

  

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

  Tags: Convert, fasta

  1919 days ago

• • Jit@jit.aber

  

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

  Tags: Convert, AB12SCF, SCF, AB1

  1918 days ago

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