User: Carlos Caicedo

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Location:
Colombia/Universidad de Antioquia
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52 seconds ago
Joined:
8 months, 3 weeks ago
Email:
c***********@unal.edu.co

Posts by Carlos Caicedo

<prev • 18 results • page 1 of 2 • next >
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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 3 days ago by Carlos Caicedo50
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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 4 days ago by Carlos Caicedo50
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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 6 days ago by Carlos Caicedo50
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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 7 days ago by Carlos Caicedo50 • updated 7 days ago by Jacob Warner290
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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 27 days ago by Carlos Caicedo50
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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 27 days ago by Carlos Caicedo50
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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 27 days ago by Carlos Caicedo50
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How to know if a genome is curated?
... Dear all I am going to work with E. coli k-12 sub-strain mg1655. In the PATRIC website I found more than 10 genomes available. How can I know what is the best curated genome? and which is the most used? Thanks Carlos ...
genome assembly written 11 weeks ago by Carlos Caicedo50 • updated 11 weeks ago by Brian Bushnell11k
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Comment: C: Transcriptome assembly evaluation with transrate
... Yes, I did. I was running the tutorial `$ transrate --assembly transcripts.fa` It worked well. But, when I tried to run $ transrate --assembly transcripts.fa \ --left left.fq \ --right right.fq It did not executed. ...
written 3 months ago by Carlos Caicedo50
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Comment: C: Transcriptome assembly evaluation with transrate
... When I run `transrate --install-deps all` I get this message: usuario@FINGNVO18-228CC:~$ transrate --install-deps all [ERROR] 2017-02-08 15:22:39 : install-deps all is not valid. You must specify one of: ref And, when I run usuario@FINGNVO18-228CC:~$ transrate --install-deps ref ...
written 3 months ago by Carlos Caicedo50

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

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