User: Carlos Caicedo

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80
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Colombia/Universidad de Antioquia
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3 days, 22 hours ago
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9 months, 3 weeks ago
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c***********@unal.edu.co

Posts by Carlos Caicedo

<prev • 21 results • page 1 of 3 • next >
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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 13 days ago by Carlos Caicedo80
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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 24 days ago by Carlos Caicedo80
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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 25 days ago by Carlos Caicedo80
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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 weeks ago by Carlos Caicedo80
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Processing of assembled transcriptome
... Dear all I am performing some steps after assembly of transcriptome with Trinity with the idea of obtaining the best quality possible of the transcriptome. I searched for vector contamination with VecScreen, removed the redundancy with CD-HIT and BlastClust, and removed chimeras with CD-HIT-DUP an ...
assembly rna-seq written 5 weeks ago by Carlos Caicedo80
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Answer: A: How to know that your RNA-seq is stranded or not?
... Hi This image could help. https://galaxyproject.org/tutorials/rb_rnaseq/stranded_result.png In stranded example reads are clearly stratified between the two strands Of course, you need to perform the alignments, get the BAM file and visualize it in any of the software available (SeqMonk, RNAseqV ...
written 5 weeks ago by Carlos Caicedo80
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Downloading from nr data base.
... Dear all I would like to download the genes information for the streptomyces genus from the nr database. I tried to do it but I downloaded all the database. Could someone explain me how to filter out the data to only get the information for streptomyces? Thanks Carlos ...
gene written 5 weeks ago by Carlos Caicedo80 • updated 5 weeks ago by Jacob Warner310
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Comment: C: rna-seq alignment and calculate + compare expression levels
... Hi From Wikipedia: Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initi ...
written 8 weeks ago by Carlos Caicedo80
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Answer: A: rna-seq alignment and calculate + compare expression levels
... Hi Have you ever thought about use Galaxy ? All the tools that you mentioned are available there and you do not need to use command line. Regards ...
written 8 weeks ago by Carlos Caicedo80
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Answer: A: assembly through trinity
... Hi. How it was mentioned by st.ph.n the simplest way to get assembly stats is using the comand Trinity_stats.pl that come available with Trinity, but you need to instal Trinity in your computer. I do not know if the Galaxy wrapper of Trinity has this available. The best way is ask at https://bios ...
written 8 weeks ago by Carlos Caicedo80

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Teacher 4 months ago, created an answer with at least 3 up-votes. For A: transcriptome assembly evaluation

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