User: ugurcabuk

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ugurcabuk130
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130
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Turkey
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1 month, 1 week ago
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2 years, 5 months ago
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Posts by ugurcabuk

<prev • 39 results • page 1 of 4 • next >
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Comment: C: IDBA-UD Output Question
... What is your input ? IDBA gives some contigs.fa files which are depends on k-mer size you entered as input. Also, there sould be one scaffold.fa as output. What is your parameters ? Give more information please ...
written 11 weeks ago by ugurcabuk130
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Comment: C: Missing pseudogenes in annotation report
... 1. please, make sure the file is executable. If not, you can do it using `chmod +x`. Or you can call it through `python pgap.py`. 2. some descriptions about yaml file is on the tool's github page, wiki section. See the link. [Input-files][1] [1]: https://github.com/ncbi/pgap/wiki/Input-Files ...
written 3 months ago by ugurcabuk130
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Comment: C: Missing pseudogenes in annotation report
... Hi Seraph, I think, you can send an e-mail to NCBI submission portal (http://genomes@ncbi.nlm.nih.gov) about it. By the way, I found something that can be useful. See the link. [PGAP][1] [1]: https://github.com/ncbi/pgap ...
written 3 months ago by ugurcabuk130
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Comment: C: Missing pseudogenes in annotation report
... As far as I know, PROKKA does not give you pseudogenes in the genome. You should manually focus on pseudogenes, such as C, N-terminus missing fragmented on ORF. However, I do not know If there is another method to find pseudogenes in the genome. ...
written 3 months ago by ugurcabuk130
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Comment: A: Comparing SPAdes assemblies to each other?
... I think, [Quast][1] work for you. All you need to do is to check the parameters. It has got alignment parameter. [1]: http://bioinf.spbau.ru/quast ...
written 3 months ago by ugurcabuk130
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Comment: C: Why one genome assembly is more fragmented than others?
... I don't know exactly what the reason is but did you assessment your all assemblies using BUSCO tool ? Maybe in the genome assembly you mentioned contains contamination or missing in your raw data ? ...
written 3 months ago by ugurcabuk130
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Answer: A: Display bootstraps on tree RAxML-NG
... check the link I answered kind of the same question in the forum https://www.biostars.org/p/446023/#446027 ...
written 3 months ago by ugurcabuk130
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Comment: C: Find transcripts of one species in RNA-assembly
... I would recommned you that, at least my approach, firstly classify the reads using kraken and then assembled them. After classifying them, whichever species you want to extract from the reads can be filtered based on taxonomy id in the file. ...
written 3 months ago by ugurcabuk130
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Answer: A: reorder contigs into scaffold?
... What kind of organism ? Please, give more information. However, There are some tools to make it. [Contiguator][1] [ABACAS][2] [Mauve][3] If it is bacteria, the article, [Approaches for in silico finishing of microbial genome sequences][4], can give you some ideas [1]: http://contiguator.sou ...
written 3 months ago by ugurcabuk130
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Comment: C: Is the ssGSEA enrichment score affected by other samples in the analysis group?
... It is interesting.. I haven't never seen such a issue since I have run it. But you can also use the other packages for single sample analysis. I would recommend you to try [GSVA][1] and [Singscore][2] [1]: https://bioconductor.org/packages/release/bioc/html/GSVA.html [2]: https://bioconductor. ...
written 4 months ago by ugurcabuk130

Latest awards to ugurcabuk

Popular Question 3 months ago, created a question with more than 1,000 views. For GSVA and SSGSEA for RNA-Seq TPM data
Popular Question 3 months ago, created a question with more than 1,000 views. For GSVA and SSGSEA for RNA-Seq TPM data
Scholar 3 months ago, created an answer that has been accepted. For A: How to filter BLAST results by query coverage? How to analyze large BLAST output
Scholar 4 months ago, created an answer that has been accepted. For A: How to filter BLAST results by query coverage? How to analyze large BLAST output
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to filter BLAST results by query coverage? How to analyze large BLAST output

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