Question: Remove Duplicate Reads From Fasta File
0
gravatar for deepthithomaskannan
4.8 years ago by
Canada
deepthithomaskannan190 wrote:

Hi all,

I want to remove duplicate reads from my fasta file. I tried to use fastx_collapser. But since my reads contains lowercase letters and hyphens it failed.

Please help.

Thanks,D.

fasta read • 4.3k views
ADD COMMENTlink modified 5 months ago by Eslam Samir90 • written 4.8 years ago by deepthithomaskannan190

duplicate of:

How to remove the same sequences in the FASTA files?

ADD REPLYlink written 4.8 years ago by Pierre Lindenbaum96k

It's like everybody wants to remove duplicates here!

ADD REPLYlink written 4.8 years ago by Manu Prestat3.8k
2
gravatar for Manu Prestat
4.8 years ago by
Manu Prestat3.8k
Marseille, France
Manu Prestat3.8k wrote:

Try the sequniq tool from the GenomeTools suite:

gt sequniq -o output.fasta input.fasta
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Manu Prestat3.8k

i tried this command, plz could u tell how this command applied...

ADD REPLYlink written 2.1 years ago by Manoj20
1
gravatar for Rm
4.8 years ago by
Rm7.5k
Danville, PA
Rm7.5k wrote:

Try CD-hit or Uclust

You can remove unwanted hyphens and convert to uppercase using sed:

echo FaSta-TEst | sed "s/-//g ; s/(.*)/\U&/g"

ADD COMMENTlink written 4.8 years ago by Rm7.5k

Or just tr: echo FaSta-TEst | tr -d - | tr 'a-z' 'A-Z'

ADD REPLYlink written 4.8 years ago by Ketil3.8k
0
gravatar for Eslam Samir
5 months ago by
Eslam Samir90
Egypt / Cairo / Microbiology & Immunology Department
Eslam Samir90 wrote:

Here is my free program on Github Sequence database curator (https://github.com/Eslam-Samir-Ragab/Sequence-database-curator)

It is a very fast program and it can deal with:

  1. Nucleotide sequences
  2. Protein sequences

It can work under Operating systems:

  1. Windows
  2. Mac
  3. Linux

It also works for:

  1. Fasta format
  2. Fastq format

Best Regards

ADD COMMENTlink written 5 months ago by Eslam Samir90
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