User: Iñigo Prada

gravatar for Iñigo Prada
Iñigo Prada200
Reputation:
200
Status:
Trusted
Location:
Denmark/University of Copenagen
Last seen:
3 days, 2 hours ago
Joined:
9 months, 3 weeks ago
Email:
p*******@hotmail.es

I am a second year Bioinformatics student and a student assistant/ Bioinformatician at the University of Copenhagen

Posts by Iñigo Prada

<prev • 56 results • page 1 of 6 • next >
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Answer: A: Biopython: Retrieving atomic coordinates of a model from a pdb file
... The error you posted does not match with the code posted. In the error, in line 12 the code is: coord=model.get_coord() And in the code in line 12 you have: coord=atoms.get_coord() The code you posted should work fine,as get_coord() is an instance of the atom class. could you update the ...
written 6 days ago by Iñigo Prada200
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Comment: C: Mapping RNA-Seq data on genome from another species
... Here you have a very good review about how to do NGS analysis with non-model organisms. It has a part on RNA-seq and how to deal with situations were you do not have a reference genome[Next-generation biology: Sequencing and data analysis approaches for non-model organisms][1] [1]: http://www.sc ...
written 10 days ago by Iñigo Prada200
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Comment: C: Downloading aUTRs from RefSeq
... I asked a similar question about how to get the UTR of a set of genes in this [post][1]. If you want to map those transcripts to affymetrix probe sets, you have to index the probes and align them using an aligner. [1]: https://www.biostars.org/p/206407/ ...
written 19 days ago by Iñigo Prada200
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Comment: C: A long run time problem
... Working with a interpreted language like python will always make your code slower. It seems that your problem could be easily paralellized. Give a look at the multiprocessing package or to GNU Parallel. ...
written 21 days ago by Iñigo Prada200
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Comment: C: Differential expression analysis 5 conditions 3 replicates each matrix counts
... Could you clarify your experimental design? My guess would by that dpi is Days Post Infection, and you you have 3 biological replicates for each condition (infected with bacteria,naive...) at different times (2 days,7 days...) , if this is okay, the experimental design is crucial for creating a DE ...
written 25 days ago by Iñigo Prada200
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Comment: C: bedtools_intersect files sorting problem
... Depending in your error, you may need to sort the bam file. You will need to add more info to the question in case you want some help ...
written 5 weeks ago by Iñigo Prada200
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Comment: C: bedtools_intersect files sorting problem
... How did you sort the bam file? ...
written 5 weeks ago by Iñigo Prada200
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Comment: C: What are the various procedures involved in DNA Mapping ?
... exactly. The sam format has a lot of information about the alignment like mapping quality... ...
written 5 weeks ago by Iñigo Prada200
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Comment: C: What are the various procedures involved in DNA Mapping ?
... I would begin reading this [How to map billions of short reads onto genomes][1]. And then I would google how to use a given aligner. I recommend you to use bwa-mem. Here is an overview of the commands [bwa][2]. The input to an aligner is a fastq file, and the output is sam/bam file. [1]: https:/ ...
written 5 weeks ago by Iñigo Prada200
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Answer: A: how to select with unix a column by the column name in a txt files
... `awk '{print $column_number}' your_file.txt` For example, if you want to get column 3: `awk {print $3}' your_file.txt` ...
written 5 weeks ago by Iñigo Prada200

Latest awards to Iñigo Prada

Supporter 4 months ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.

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