BOL: Wire posts tagged with 'Fasta'

Wire post by Radha Agarkar

Radha Agarkar — Sun, 03 Dec 2017 15:39:46 -0600

Remove the fasta with zero size: awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} $2 {print ">"$0}' input.fas > output.fas #fasta #remove

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

Wire post by Neel

Neel — Wed, 02 Aug 2017 04:50:14 -0500

Reformat you fasta sequence with size. $ seqkit seq -w 50 allGenomeContacted.fa > allGenomeContacted_final.fa #Reformat #Fasta #Size

Wire post by Rahul Nayak

Rahul Nayak — Wed, 19 Jul 2017 08:26:23 -0500

Remove "|" from fasta header. $ sed 's,|,_,g' -i file.fa #fasta #header #sed

Wire post by Rahul Nayak

Rahul Nayak — Wed, 19 Jul 2017 08:22:57 -0500

Remove unwanted character from fasta file. sed -e '/^[^>]/s/[^ATGCatgc]/N/g' file.fa #fasta #file #header #charater

Wire post by Jit

Jit — Thu, 06 Jul 2017 14:35:32 -0500

Remove the unnecessary #fasta #header. $ sed 's/\s.*$//' Adineta_vaga_v2.0.scaffolds.fa > new_file.fasta

Wire post by Rahul Nayak

Rahul Nayak — Fri, 23 Jun 2017 05:06:43 -0500

Count the number of bases in fasta file. grep -v ">" file.fasta | wc | awk '{print $3-$1}' #Fasta #Count #Bases

Wire post by Jit

Jit — Sun, 18 Jun 2017 14:14:13 -0500

Append the string to fasta header. $ sed 's/>.*/&_Bacteria/' foo.in > out.fasta #Sed #Fasta #String #Append

Wire post by Jit

Jit — Tue, 30 May 2017 05:17:21 -0500

Filter #blank #lines from a #fasta file using sed. $ sed '/^$/d' finalSample.fa > finalSample_filtered.fa #Linux #Filter #FASTA #SED

Wire post by Abhimanyu Singh

Abhimanyu Singh — Thu, 11 May 2017 10:43:18 -0500

fastq to fasta convertor $ sed -n '1~4s/^@/>/p;2~4p' test.fastq > test.fasta #Convert #Fasta #Fastq #fa #fq

Wire post by Jit

Jit — Fri, 21 Apr 2017 08:28:28 -0500

To clean up a fasta file so only first column of the header is outputted:$ awk '{print $1}' file.fa > output.fa #Sed #Clean #Header #Fasta

Wire post by Jit

Jit — Fri, 21 Apr 2017 08:24:53 -0500

To add something to end of all header lines: $ sed 's/>.*/&WHATEVERYOUWANT/' file.fa > outfile.fa #Add #Fasta

Wire post by Jit

Jit — Wed, 08 Mar 2017 08:11:52 -0600

Get the fasta sequence of the coordinates http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html #Fasta #Bed #Coordinates #Bedtools

Wire post by Shruti Paniwala

Shruti Paniwala — Wed, 26 Oct 2016 09:24:08 -0500

Extract a fasta sequence from multifasta file: samtools faidx multitest.fa and then samtools faidx multitest.fa fasta_id > out.fa #Samtools #Fasta #Extract #Multifasta

Wire post by Radha Agarkar

Radha Agarkar — Fri, 16 Sep 2016 02:57:36 -0500

Extract fasta sequence by Ids: perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #Perl #PerlOneliner #PerlTrick #Extract #Ids #Fasta