This is a test version of Biostars. For the public version, visit https://www.biostars.org.
sequence head change!

Hi, I have a lot of like as 

HWI-ST1234:231:H2CNTADXY:1:1101:6127:2223       ACGAATCCGTGCGACGTGGGGCTGGAT     71
HWI-ST1234:231:H2CNTADXY:1:1101:19654:2083      CCTTTCTCCTCTTCGGCCTTCAAAGTTC    63.

I want to change to format like as

>HWI-ST1234:231:H2CNTADXY:1:1101:6127:2223 71
ACGAATCCGTGCGACGTGGGGCTGGAT
>HWI-ST1234:231:H2CNTADXY:1:1101:19654:2083 63
CCTTTCTCCTCTTCGGCCTTCAAAGTTC

Have some ways do like this for a lot of sequence? Thanks Fuyou

rna-seq
• 2,487 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by fufuyou fufuyou

It's not immediately clear to me what has to be changed and what format your data is in...

• 2 views • link
written by WouterDeCoster WouterDeCoster

2 answers 

awk '{printf(">%s %s\n%s\n",$1,$3,$2);}' in > out

and that's not much different from a previous answer for a question you asked: C: Add a sequence name!

• 2 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks. It works.

• 2 views • link
written by fufuyou fufuyou

so mark this question as answered, (icon on the left), as well as your previous question. Thanks.

• 2 views • link
written by Pierre Lindenbaum Pierre Lindenbaum 
awk -F " " '{print">"$1,$3,$2"\n>"$4,$6,$5}' in.fastq > out.fastq
• 2 views • link
written by rbagnall rbagnall

Hi rbagnall, Thanks, your results is HWI-ST1234:231:H2CNTADXY:1:1101:6127:2223 71 ACGAATCCGTGCGACGTGGGGCTGGAT , it is not like

HWI-ST1234:231:H2CNTADXY:1:1101:6127:2223 71 ACGAATCCGTGCGACGTGGGGCTGGAT.

• 2 views • link
written by fufuyou fufuyou

Thanks Rbagnall. It works well. Fuyou

• 0 views • link
written by fufuyou fufuyou

Log in to answer this question.

More posts like this
  • Generating artificial NGS reads from a FASTA file specifying read length, coverage, and start seque…
    written by Hamish • Hamish
    I am looking to generate artificial single-end Illumina sequencing data from a FASTA containing a number of short sequences representing unique molecular identifiers. However, I've …
  • Extraction sequence from other sequence
    written by fufuyou fufuyou
    Hello， I have lots of sequences from two parts: one is >seqeunce1 ATGTGTGTTGTACAACTTTGGTATATACTGTATATACC42327477R_3222148F_10594369R_21575807R_1679947F_28391165R other is >42327477R_3222148F_10594369R_21575807R_1679947F_28391165R TGTGTTGTACAACTTTGGTATATACTGTATATACC I want to get the sequence like as …
  • How To Rename FASTA Headers
    written by mollysil • mollysil
    Hi, I have very little experience with scripts. I want to change my FASTA sequence headers (I have 100's of FASTA sequences per file) from …
  • merge multiple fasta sequences in two files into a single file line by line
    written by girijakaushal • girijakaushal
    Hello, I need to combine two fasta files having thousands of fasta sequences like: File1: >HWI-700823F:57:C97D4ANXX:8:1101:1295:2240 2:N:0:GTGAAACG NAAGAGGGGAATCAGGAGGGACCGCAAATATGCAGTGCAGCCCCGTGCCGTGTATGCAAC TGGGGTACACATGTCCCAGAACATAGCCGGGAAGTCAACG >HWI-700823F:57:C97D4ANXX:8:1101:1587:2235 2:N:0:GTGAAACG NTCTGCCGCTCTGCGTACAAGCTTGAGAGTTTTTTTGCAGACCTTCTTGCCGGCGAGAGG CTTAGCTATGGGAGCCAAAGCCATCATCTTCTTCTTCTCT >HWI-700823F:57:C97D4ANXX:8:1101:1974:2229 2:N:0:NTGAAANN …
  • Add a sequence name!
    written by fufuyou fufuyou
    Hi, I get my sequence files like this TAACAGTGGGTCGAGATAAGGAC 1 CGCCCGGACGTCAGAGAAAAAGGTGCCAGCGCGGCGCAGAGAATGGAATT 1 TTAGTATGACGGGCTGACACGAGA 3 I want to add a sequence name at each sequence file …
  • how to get the genotypes from vcf file.
    written by fufuyou fufuyou
    Hi, I have a vcf files with multiple samples. I want get the genotype data from the vcf file. I do not know how to …
  • Extract the DNA sequence header!
    written by fufuyou fufuyou
    I have question about our DNA sequence data. If the format of sequence data is ``` @HWI-ST1234:136:C5F6VACXX:6:1101:4121:2231 1:N:0:ACTTGA TATGGGTTTCCACGGAGCACAGTGCCTAGTGCTCACTCCCCAGTTGTATCTTATTTTTCAGGTCAGCAGGTCGGGCCGGGAGTGTGACATGACGGAGCAGA + CCCFFFDDHHHHHJJGIJJJJJHIJJIJJHIJIJIJJJJJJIIIIJGIIBFHHFHJJJG>FHIJIGIIEHAHBBAB@BDBDD<?ACA>CDDDDDD5<BBD?. ``` I can extract …
  • Efficiently join paired-end read coordinates in the same line?
    written by daniel.soronellas daniel.soronellas
    Dear community, I have a huge paired-end HiC dataset (BAM format) which I want to format like this way: ``` HWI-D00283:117:C5KKJANXX:2:1101:1139:77789 chr6 153338506 153338556 37 …
  • Trim Sequences And Quality In Fastq File
    written by abn4 • abn4
    I have bunch of fastq files in the directory and i want to trim the sequence by 2 nucleotides and quality(if the read has 51 …
  • How To Understand The Encoding And Trim Their Adapters
    written by bmechuangye • bmechuangye
    <p>Hi,</p> <p>I am puzzled how to change the encode to Sanger format phred+33 of the data and how to trim the adapter sequence? I have …