Question: Software for cleaning FASTA files
0
gravatar for l.souza
22 months ago by
l.souza70
Brasilia, Brazil
l.souza70 wrote:

What software can I use to remove sequences:

  • with a lot of unkown nucleotides (N)
  • duplicated
  • too short

?

sequences alignment cleaning • 693 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by l.souza70
2

Hi Lucas Souza,

This question contains insufficient information to get answered. Please elaborate, for example on the technology used for generating the data. We are really bad at reading your mind (that's a bug in biostars which will get fixed in a next release). So for now, put some effort in your question and don't make it hard for people trying to help you.

Cheers,
Wouter

ADD REPLYlink written 22 months ago by WouterDeCoster38k

Edited. Is it better?

ADD REPLYlink written 22 months ago by l.souza70

Obviously, all information you just added is vital for answering the question. By now we have lost 9 hours since you asked the question. Remember this for further questions that it's important to be as informative as possible.

ADD REPLYlink written 22 months ago by WouterDeCoster38k

Must you use entire genomes? Are there particular genes that are perhaps informative enough?

ADD REPLYlink modified 22 months ago • written 22 months ago by genomax65k

The entire genome produces a single polyprotein that is cleaved in post-translational processes. For this reason I think it would be better to use the entire genome. But I may be wrong with this thinking

ADD REPLYlink modified 22 months ago • written 22 months ago by l.souza70

Lucas Souza : Please do not change the entire contents of an original question. That makes the chain of responses/comments here meaningless. Consider this a fair warning. I will tag @Istvan to see if he can restore the original question.

ADD REPLYlink modified 22 months ago • written 22 months ago by genomax65k

Tagging: Istvan Albert

ADD REPLYlink written 22 months ago by genomax65k
2
gravatar for Brian Bushnell
22 months ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

Hi Lucas,

You can accomplish most of what you want using the BBMap package.

Filtering Ns and short sequences:

bbduk.sh in=file.fasta out=filtered.fasta maxns=50 minlen=1000

Removing exact duplicates and containments:

dedupe.sh in=file.fasta out=deduped.fasta

Unfortunately BBDuk does not have a mechanism for removing sequences based on the % of Ns, just the absolute number, but I may add that.

ADD COMMENTlink written 22 months ago by Brian Bushnell16k
1

Wait, there is a task that none of the BB-Tools can do? :)

ADD REPLYlink written 22 months ago by finswimmer11k

Geez, like I said, I may add it :) I already wrote myself a note!

ADD REPLYlink written 22 months ago by Brian Bushnell16k
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