BOL: Wire posts tagged with 'fastaq'

Wire post by Surabhi Chaudhary

Surabhi Chaudhary — Wed, 23 Mar 2016 05:48:58 -0500

#BAM file to #fastaq #conversion with #Samtool: samtools view filename.bam | awk '{OFS="\t"; print "@"$1"\n"$10"\n+\n"$11}' >| filename.fastq

Wire post by Rahul Nayak

Rahul Nayak — Wed, 09 Sep 2015 16:17:11 -0500

Count the number of sequences in fastaq file. grep -c '^@' sample1.fq #Fastaq #Count #Number #Grep #Dirty #Oneliner #NGS

Wire post by Jitendra Narayan

Jitendra Narayan — Fri, 30 May 2014 06:08:14 -0500

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. https://github.com/lh3/seqtk #FASTA #FASTAQ #NGS

Wire post by Jit

Jit — Fri, 23 May 2014 10:10:20 -0500

FastaQ 2 Fasta Oneliner: paste - - - -< totalRNA_placental_1.fastq | perl -pale'$_="@F[0..1]"'|tr "\^@" "\>" | perl -pale 's/\s/\n/g' #Oneliner #NGS #FastaQ #Fasta

Wire post by Neel

Neel — Mon, 12 May 2014 04:47:30 -0500

zcat input_file.fastq.gz | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > output_file.fa #fastaQ2fasta #fastaq #fasta #Oneliner