User: Hugo

gravatar for Hugo
Hugo140
Reputation:
140
Status:
Trusted
Location:
Universidade de Vigo, Ourense (Spain)
Website:
http://www.sing-group....
Last seen:
3 days, 7 hours ago
Joined:
1 year, 4 months ago
Email:
h******@gmail.com

Posts by Hugo

<prev • 46 results • page 1 of 5 • next >
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Comment: C: Extract sequence ID from Fasta for a given sequence
... Dear MAPK, if you usually work with FASTA files you may find SEDA (http://www.sing-group.org/seda/) an useful tool. It has a great variety of operations to manipulate, filter, and transform FASTA files (check out the manual to see all of them: https://www.sing-group.org/seda/manual/index.html). It a ...
written 8 weeks ago by Hugo140
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Comment: C: Find all fragments of n length in a larger sequence
... Dear myrmex, you may be interested in having a look at our SEDA software (https://www.sing-group.org/seda/download.html). It contains several functions for filter, transformation, and manipulation of FASTA files, including operations to perform batch BLAST queries (https://www.sing-group.org/seda/ma ...
written 10 weeks ago by Hugo140
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Answer: A: how to change fasta headers?
... Dear colleague, I think that you may also find useful the **SEDA** software (http://sing-group.org/seda/ ). As you can see in the manual (https://www.sing-group.org/seda/manual ), it has a lot of different customizable operations to process FASTA files, including operations to reformat sequence he ...
written 12 weeks ago by Hugo140 • updated 12 weeks ago by finswimmer8.0k
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Comment: C: How to concatenate multiple fasta file
... Hi, **SEDA** (https://www.sing-group.org/seda) has an operation named *"Concatenate sequences"* (https://www.sing-group.org/seda/manual/operations.html#concatenate-sequences) aimed to do what you ask for. However, to use it, you need that the sequence names or identifiers to be identical, so you wil ...
written 4 months ago by Hugo140
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Comment: C: Removing gaps from fasta sequence file
... Hi, you can also use the "Undo alignment" function of the SEDA software (https://www.sing-group.org/seda/manual/operations.html#undo-alignment). Regards. ...
written 4 months ago by Hugo140
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Comment: C: Remove sequences <300 bases from FASTA file
... Other people gave you excellent solutions. Nevertheless, you may be also interested in **SEDA** (http://www.sing-group.org/seda/ ), an open-source tool for processing FASTA files. Among other functions, it provides an operation to apply different filters, including sequence length (https://www.sing- ...
written 4 months ago by Hugo140 • updated 4 months ago by finswimmer8.0k
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Comment: C: Tuxedo RNA Seq Novice Please Help
... As a complement to previous answers, **DEWE** (http://sing-group.org/dewe/) offers a user-friendly GUI to run the HISAT2, StringTie and Ballgown workflow, with the addition of edgeR to the DE analysis stage. It also produces a rich variety of outputs related with the DE results. Regards. ...
written 5 months ago by Hugo140
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Comment: C: extracting the longest transcript in a fasta file
... You can sort the FASTA by sequence length using SEDA (http://www.sing-group.org/seda/manual/operations.html#sort) and then take the longest sequence(s). ...
written 6 months ago by Hugo140
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Answer: A: Retrieve multi-line fasta sequences using list of locus tag
... Hello sharmatina189059, for this type of operations you can use **SEDA** (http://www.sing-group.org/seda/). Specifically, the *"Pattern filtering"* operation (http://www.sing-group.org/seda/manual/operations.html#pattern-filtering) allows to do what you are asking for. You only need to load your ...
written 6 months ago by Hugo140
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Comment: C: Help with rat RNA-Seq data with the HISAT-StringTie workflow
... Dear colleague, I can't help you with this issue and I hope others can help you. Nevertheless, I would like to kindly ask you to try our DEWE tool (http://www.sing-group.org/dewe) to run your analysis. DEWE offers an easy way to run that workflow (HISAT2, StringTie and Ballgown) and we would be plea ...
written 6 months ago by Hugo140

Latest awards to Hugo

Scholar 8 months ago, created an answer that has been accepted. For A: Renaming FASTA headers while keeping some previous information?
Scholar 10 months ago, created an answer that has been accepted. For C: Ballgown data reading problem
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Renaming FASTA headers while keeping some previous information?
Scholar 10 months ago, created an answer that has been accepted. For C: Ballgown data reading problem

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