User: Hugo

gravatar for Hugo
Hugo110
Reputation:
110
Status:
Trusted
Location:
Universidade de Vigo, Ourense (Spain)
Website:
http://www.sing-group....
Last seen:
17 hours ago
Joined:
11 months, 2 weeks ago
Email:
h******@gmail.com

Posts by Hugo

<prev • 40 results • page 1 of 4 • next >
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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 23 days ago by Hugo110
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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 5 weeks ago by Hugo110
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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 weeks ago by Hugo110
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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 7 weeks ago by Hugo110
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Comment: C: Fast site removal
... I have updated my answer, hope this can be useful to you. ...
written 7 weeks ago by Hugo110
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Comment: C: Fast site removal
... Ok, I understand now. How is your AA file? I think that you should use this awk filter first and then filter the remaining sites. Please, show us your AA file to see how this can be achieved. ...
written 7 weeks ago by Hugo110
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Answer: A: Fast site removal
... You can use **awk** in first place to obtain the list of sites. For instance, the following command prints only lines where "C_Rate" (fourth column, $4 in awk) is higher or equal than 1: awk 'NR > 1 { if ($4 >= 1) print $0 }' sites.list I would recommend you to get only the first column ...
written 7 weeks ago by Hugo110 • updated 7 weeks ago by genomax51k
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Answer: A: Selecting defined length fasta sequence and excluding them from a dataset
... You can use SEDA (http://www.sing-group.org/seda/), which has an option to filter sequences by length (http://www.sing-group.org/seda/manual/operations.html#filtering) as well as other types of filtering. Regards. ...
written 8 weeks ago by Hugo110
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Comment: C: headers from multifasta files
... You are absolutely right Kevin, I have upvoted it ;-) ...
written 9 weeks ago by Hugo110
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Comment: C: headers from multifasta files
... Hi Ulises, although this can be easily achieved as other people has already explained, if you are working with FASTA files you may be interested in **SEDA** (http://www.sing-group.org/seda/). Please, take a look and feel free to contact us if you need some assistance using it. Regards. ...
written 9 weeks ago by Hugo110

Latest awards to Hugo

Scholar 3 months ago, created an answer that has been accepted. For A: Renaming FASTA headers while keeping some previous information?
Scholar 5 months ago, created an answer that has been accepted. For C: Ballgown data reading problem
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Renaming FASTA headers while keeping some previous information?
Scholar 5 months ago, created an answer that has been accepted. For C: Ballgown data reading problem

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