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The Wire
#ids
Wire posts tagged with 'ids'
Jit
@jit.aber
Thread
By
Jit
2146 days ago
Extract sequence by ids $ xargs samtools faidx Adineta_vaga.v2.pep.fa < AlienIds > allAlienSeq.fa
#Extract
#Ids
#Sequences
Manisha Mishra
@manisha
Thread
By
Manisha Mishra
2391 days ago
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
Manisha Mishra
@manisha
Thread
By
Manisha Mishra
2391 days ago
Extract fasta with Ids. $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file
#extract
#fasta
#sequence
#ids
Poonam Mahapatra
@poonam
Thread
By
Poonam Mahapatra
2518 days ago
Remove duplicate fasta ids: awk '/^>/{f=!d[$1];d[$1]=1}f' in.fa > out.fa
#duplicate
#fasta
#ids
Radha Agarkar
@radhaagarkar
Thread
By
Radha Agarkar
2970 days ago
Extract sequence by using Ids file (assuming one ids in a line): perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if
@ARGV
' ids.file fasta.file
#PerlTricks
#PerlOneliner
#Perl
#Extract
#Ids
#
Radha Agarkar
@radhaagarkar
Thread
By
Radha Agarkar
2970 days ago
Extract fasta sequence by Ids: perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file
#Perl
#PerlOneliner
#PerlTrick
#Extract
#Ids
#Fasta
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
3342 days ago
Extract sequences by their ID from a fasta file. perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if
@ARGV
' ids.txt sample1.fa
#Extract
#Sequences
#IDs
#Fasta
#Perl
#Trick
#Oneliner
Jit
@jit.aber
Thread
By
Jit
3816 days ago
Extract list of read ID from bam file: samtools view mbi.sorted.bam |perl -ne '/ID/ && print' > extractedID.sam
#Extract
#Ids
#SAM
#BAM
#NGS