User: Carlos Caicedo

gravatar for Carlos Caicedo
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Colombia/Universidad de Antioquia
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1 day, 15 hours ago
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1 year, 1 month ago
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c***********@unal.edu.co

Posts by Carlos Caicedo

<prev • 27 results • page 1 of 3 • next >
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Answer: A: Drawing Venn Diagram
... Recently, I was exploring [Vennmaster][1] [1]: http://sysbio.uni-ulm.de/?Software:VennMaster ...
written 6 weeks ago by Carlos Caicedo120
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Comment: C: HMMER: Failed to open target sequence database for reading
... Hi cayro Did you prepare your database with `hmmpress`? `hmmpress` creates four binary files. The database cannot be read because it needs to have those four auxiliary binary files generated by hmmpress. ...
written 6 weeks ago by Carlos Caicedo120
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Comment: C: How can I get Transcript ID from the gene ID?
... Of course, you are right. I going to try to do a better explanation of my question. A gff file is something like this: chromosome ena gene 661 1041 . - . ID=gene:SCLAV_0001;biotype=protein_coding;description=Hypothetical protein;gene_id=SCLAV_0001;logic_name=ena;version=1 chromosome ena tr ...
written 7 weeks ago by Carlos Caicedo120 • updated 7 weeks ago by genomax34k
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Comment: C: How can I get Transcript ID from the gene ID?
... I have a data from a bacterium specie, so I think BioMart does not function in this case. ...
written 7 weeks ago by Carlos Caicedo120
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How can I get Transcript ID from the gene ID?
... Dear all I have a list of gene IDs in a tabular format. How I can extract the transcript IDs for the list of genes IDs mentioned above, from a gff file? Thank you so much. Carlos ...
rna-seq written 7 weeks ago by Carlos Caicedo120 • updated 7 weeks ago by Jeffin Rockey400
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Answer: A: Understanding de-novo transcriptome assembly quality using Transrate
... In [THIS][1] page the developers of transrate explain the significance of the metrics obtained with the software and the ideal value for each metrics. Personally, I think that you TRANSRATE ASSEMBLY SCORE is very low and also the fragments mapped (That means, only 57 % of the reads are being used ...
written 3 months ago by Carlos Caicedo120
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Answer: A: How to remove rRNA, bacterial RNA and polyA contamination from RNA-seq data(fast
... [SortMeRNA][1] could help you. It was developed to filter ribosomal RNA. In addition, it give you an idea of how serious is the contamination because you obtain a percent of the reads aligned to ribosomal RNA. [1]: http://bioinfo.lifl.fr/RNA/sortmerna/ ...
written 4 months ago by Carlos Caicedo120
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Answer: A: Best Programs for transcript counts
... [RNA-skim][1] is another alternative that use a different approach. It partitions the transcriptome into disjoint transcript clusters based on sequence similarity and introduces the notion of sig-mers that are a special type of k-mers uniquely associated with each cluster. It was developed for RNA ...
written 4 months ago by Carlos Caicedo120
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Answer: A: RNA-seq power analysis
... [This paper][1] may help. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201821/ ...
written 4 months ago by Carlos Caicedo120
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Comment: C: Processing of assembled transcriptome
... Hi I did so and found around 2000 transcripts that have a hit with less than 50%. What can I conclude from that result? Should I discard those transcripts? ...
written 5 months ago by Carlos Caicedo120

Latest awards to Carlos Caicedo

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: transcriptome assembly evaluation

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