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The Wire
#FASTA
Wire posts tagged with 'FASTA'
Radha Agarkar
@radhaagarkar
Thread
By
Radha Agarkar
2350 days ago
Remove the fasta with zero size: awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} $2 {print ">"$0}' input.fas > output.fas
#fasta
#remove
Jit
@jit.aber
Thread
By
Jit
2360 days ago
Fastq 2 fasta. $ sed -n '1~4s/^@/>/p;2~4p' test.fastq > test.fasta
#fastq
#fasta
#convert
Neelam Jha
@neelam
Thread
By
Neelam Jha
2473 days ago
Reformat you fasta sequence with size. $ seqkit seq -w 50 allGenomeContacted.fa > allGenomeContacted_final.fa
#Reformat
#Fasta
#Size
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
2487 days ago
Remove "|" from fasta header. $ sed 's,|,_,g' -i file.fa
#fasta
#header
#sed
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
2487 days ago
Remove unwanted character from fasta file. sed -e '/^[^>]/s/[^ATGCatgc]/N/g' file.fa
#fasta
#file
#header
#charater
Jit
@jit.aber
Thread
By
Jit
2500 days ago
Remove the unnecessary
#fasta
#header
. $ sed 's/\s.*$//' Adineta_vaga_v2.0.scaffolds.fa > new_file.fasta
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
2513 days ago
Count the number of bases in fasta file. grep -v ">" file.fasta | wc | awk '{print $3-$1}'
#Fasta
#Count
#Bases
Jit
@jit.aber
Thread
By
Jit
2518 days ago
Append the string to fasta header. $ sed 's/>.*/&_Bacteria/' foo.in > out.fasta
#Sed
#Fasta
#String
#Append
Jit
@jit.aber
Thread
By
Jit
2537 days ago
Filter
#blank
#lines
from a
#fasta
file using sed. $ sed '/^$/d' finalSample.fa > finalSample_filtered.fa
#Linux
#Filter
#FASTA
#SED
Abhimanyu Singh
@abhimanyu
Thread
By
Abhimanyu Singh
2556 days ago
fastq to fasta convertor $ sed -n '1~4s/^@/>/p;2~4p' test.fastq > test.fasta
#Convert
#Fasta
#Fastq
#fa
#fq
Jit
@jit.aber
Thread
By
Jit
2576 days ago
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
Jit
@jit.aber
Thread
By
Jit
2576 days ago
To add something to end of all header lines: $ sed 's/>.*/&WHATEVERYOUWANT/' file.fa > outfile.fa
#Add
#Fasta
Jit
@jit.aber
Thread
By
Jit
2620 days ago
Get the fasta sequence of the coordinates
http:/
/
bedtools.readthedocs.io/
en/
latest/
content/
tools/
getfasta.html
#Fasta
#Bed
#Coordinates
#Bedtools
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2753 days ago
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
Radha Agarkar
@radhaagarkar
Thread
By
Radha Agarkar
2793 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
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