BOL: Wire posts tagged with 'Extract'

Wire post by Jit

Jit — Mon, 11 Feb 2019 18:01:41 -0600

Extract fasta with pattern $ perl -n -e '$on=(/^>(A)/) if (/^>/); print $_ if ($on);' pilonCor_round1.fasta > A_set.fa
#Pattern #Extract #Fasta

Wire post by Rahul Nayak

Rahul Nayak — Thu, 31 Jan 2019 07:19:50 -0600

This script will #extract the intron feature #gff3 and sequence from gene_exon gff3 and fasta file. Extract-intron-from-gff3

Wire post by Jit

Jit — Tue, 18 Dec 2018 04:18:32 -0600

Extract sequence by ids $ xargs samtools faidx Adineta_vaga.v2.pep.fa < AlienIds > allAlienSeq.fa #Extract #Ids #Sequences

Wire post by Rahul Agarwal

Rahul Agarwal — Sat, 12 May 2018 12:39:13 -0500

https://scrapy.org/ #extract #data #from #websites #webscraping

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 Rahul Nayak

Rahul Nayak — Wed, 28 Mar 2018 17:14:25 -0500

#Extract all the files from a #directory and #sub-dir with #pattern. $ find TrimmedDir -type f | grep "L_" | xargs -i cp {} .

Wire post by Rahul Nayak

Rahul Nayak — Wed, 14 Mar 2018 10:31:04 -0500

Get the sequences using coordinates in bed file. $ bedtools getfasta -fi input_file.fa -bed regions_file.bed #Bed #Extract #Sequence #bedtools

Wire post by Jit

Jit — Fri, 30 Jun 2017 07:16:30 -0500

Find a pattern in first 7 characters of reads. bioawk -c fastx 'substr($seq,0,7) == $TAG { print }' reads.fq.gz #Reads #NGS #Extract #Pattern

Wire post by Abhimanyu Singh

Abhimanyu Singh — Mon, 13 Mar 2017 06:13:21 -0500

#Extract a #sequence from #multi-fasta file: $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file

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 03:00:15 -0500

Extract sequence by using Ids file (assuming one ids in a line): perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.file fasta.file #PerlTricks #PerlOneliner #Perl #Extract #Ids #

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

Wire post by Poonam Mahapatra

Poonam Mahapatra — Wed, 29 Jun 2016 15:31:47 -0500

#Extract #Chromosome #Number And Start Position #Reads: samtools view bamfile.bam|awk '{print $3 "\t" $4 "\t" $4+length($10)-1}' > newfile.tab

Wire post by Poonam Mahapatra

Poonam Mahapatra — Fri, 24 Jun 2016 09:16:32 -0500

#Extract all #Reads from #BAM file for a #region Chr10:18000-45500 using #samtools: samtools view input.bam "Chr10:18000-45500" > output.bam

Wire post by Shruti Paniwala

Shruti Paniwala — Thu, 23 Jun 2016 09:00:18 -0500

#Extract #tabbed info from #BAM file with samtools: samtools view test.bam|awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $4+length($10)-1}' > file.xls