User: abascalfederico

gravatar for abascalfederico
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810
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Location:
Spain
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5 hours ago
Joined:
1 year, 8 months ago
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a**************@gmail.com

Posts by abascalfederico

<prev • 135 results • page 1 of 14 • next >
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Comment: C: nested loop to overlap two genomic ranges lists?
... Shouldn't it be `for(i in c(1:length(list.1)) {`? ...
written 4 days ago by abascalfederico810
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Comment: C: Some problems about tobacco genome
... If that happens just for some of the CDS sequences I wouldn't be very surprised. Assemblies are usually incomplete, and CDS might have been defined using RNAseq data. I would BLAST some of these CDS using NCBI's BLAST databases restricting to Nicotiana tabacum to see what's going on. ...
written 7 days ago by abascalfederico810
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Comment: C: Many to Many alignment of Large number of sequences
... Assuming you mean pairwise local alignments, I would use BLAST for this. ...
written 12 days ago by abascalfederico810
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Comment: C: Display Open Reading Frame on Clustal alignment
... This may help: with Jalview you can translate DNA alignments to amino acid alignments. The two windows communicate between them, so you can see which bases correspond to which amino acids. Jalview translates assuming reading frame is +1. If you want to modify this you could remove the first or the t ...
written 13 days ago by abascalfederico810
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Comment: C: How do you spend your time (productively) when your script is running?
... Using a loop as Pierre, but mine is less productive 0. Write the script 1. Run the script. 2. While running, calm down and have a look to the script to check everything was right. 3. Notice that providing some additional output or modifying some running condition would be great (o ...
written 13 days ago by abascalfederico810
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Comment: C: Swiss-Prot human count from the archives
... If you are referring to human entries, I guess no new proteins have been added since 2009. Or the amount of proteins removed / added is in equilibrium. If you refer to the total number of entries (any species) in Swiss-Prot, I doubt it is asymptotic since 2009. I would expect it always be growing a ...
written 14 days ago by abascalfederico810
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Comment: C: Swiss-Prot human count from the archives
... I did something like that in the past. No need for an acknowledgment. If I had to acknowledge all the people who has helped me here... ...
written 15 days ago by abascalfederico810
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Answer: A: Swiss-Prot human count from the archives
... You can read the "DT" lines from the latest Uniprot release to analyse the contents of the database along time: DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 21-JUL-1986, sequence version 1. DT 18-JAN-2017, entry version 206. ...
written 16 days ago by abascalfederico810
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Comment: C: output feature/gene name from a known base position
... IntersectBed (from bedtools) can work with bed, vcf and gff; no previous conversion needed. ...
written 17 days ago by abascalfederico810
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Comment: C: more than one annotation at a locus in SnpEff output?
... Each annotation seems to be for a different transcript. Either you have many transcripts overlapping that locus or you have a problem with the original gene annotation file. ...
written 17 days ago by abascalfederico810

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Commentator 6 days ago, created a comment with at least 3 up-votes. For C: Is it good practice to convert lowewst quality genotyes to missing?
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 4 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Student 4 months ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Scholar 4 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Centurion 8 months ago, created 100 posts.
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Is it good practice to convert lowewst quality genotyes to missing?
Supporter 11 months ago, voted at least 25 times.
Scholar 11 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 11 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 12 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 12 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 13 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
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