User: rafa.rios.50

gravatar for rafa.rios.50
rafa.rios.5060
Reputation:
60
Status:
New User
Location:
Colombia
Last seen:
1 year, 10 months ago
Joined:
4 years, 6 months ago
Email:
r***********@gmail.com

Posts by rafa.rios.50

<prev • 12 results • page 1 of 2 • next >
0
votes
1
answer
1.1k
views
1
answer
Problem with vcftools comparison, results dont make sense
... I was testing vcftools to compare variants called from different programs and obtain a consensus from the callers. But the results I'm getting just dont make any sense, thus I would like to know if there is something that I'm doing wrong. The test consisted in select the last 15 variants from my vc ...
comparison vcftools snp written 2.4 years ago by rafa.rios.5060
1
vote
2
answers
799
views
2
answers
How to split Double or Multiple Nucleotide Polymorphisms (DNP) into Single Nucleotide Polymorphisms (SNP)?
... Greetings, I have a vcf file with some variants as the following: NC_002516.2 6892 . GG AA 200.00 . . GT:CLCAD2:DP 1:0,59:59 NC_002516.2 45742 . CC TT 200.00 . . GT:CLCAD2:DP 1:0,49:58 NC_002516.2 41006 . ...
variant calling vcf snp written 2.4 years ago by rafa.rios.5060 • updated 2.4 years ago by harold.smith.tarheel4.4k
0
votes
0
answers
1.5k
views
0
answers
Comment: C: working with promoter sequence of tomato using biopython
... When you create the output file handler with the open function, use the option "a" instead of "w" to append the result to the output instead of overwritten it. ...
written 3.6 years ago by rafa.rios.5060
2
votes
1
answer
2.0k
views
1
answers
Answer: A: Problem combining ptt, rnt files
... I have this script to create the fasta, ptt and rnt files required from a genbank annotation file from the ncbi I hope it will help, it requires biopython to parse the genbank file and to write the fasta file. from Bio import SeqIO annotation_file = "" rnt_file = "" ptt_file = "" fasta_file = "" r ...
written 3.6 years ago by rafa.rios.5060
8
votes
3
answers
1.3k
views
3
answers
Is there any journal where you can post small programs to solve very specific tasks?
... Let's say you write a script for a very specific task in your work, but that could be usefull for someone else in your line of work, other bioinformaticians or biologist, and because of that you want to publish it in some journal or specialized scientific communication. Is that even possible, which ...
journal publishing paper written 3.6 years ago by rafa.rios.5060 • updated 3.6 years ago by ALchEmiXt1.9k
0
votes
1
answer
991
views
1
answers
Answer: A: Mugsy can not allocate memory
... I solved the problem, but the solution is not perfect because I am still getting other errors. What I did was to download the source code of Mugsy and re compile it. The compilation was a little buggy, there was a patch in the sourceforge repositories which worked well. Now I have an error about N ...
written 3.7 years ago by rafa.rios.5060
0
votes
0
answers
1.4k
views
0
answers
Comment: C: biopython script using MUSCLE stalls with >300 sequences
... Try adding parameters to the MuscleCommandline() function; remove the stdin parameter in the Popen() function, after that add the line: stdout, stdout = child.communicate() and remove the line SeqIO.write(prot, child.stdin, "fasta") which I dont really understand what are you doing with it because y ...
written 3.7 years ago by rafa.rios.5060
0
votes
1
answer
991
views
1
answers
Comment: C: Mugsy can not allocate memory
... I didnt expect that to be the problem, the server has 64GB in RAM, which I think is enough to do this task, even though I recompiled mugsy (I used the precompiled version) and I'm doing the alignment again to see what happens. Thanks for your suggestion I didnt know of the ps command. ...
written 3.7 years ago by rafa.rios.5060
0
votes
1
answer
991
views
1
answer
Mugsy can not allocate memory
... I'm using Mugsy to align 120 genomes but I encounter an error during the execution, the message is: Could not run system command: : Cannot allocate memory cat /../mugsy_wga_test/mugsy_out/tmpprojections.out | /source_installers/mugsy_x86-64-v1r2.2/synchain-mugsy 1000 30 30 > 62003lcbs.out 2> ...
alignment whole genome written 3.7 years ago by rafa.rios.5060
0
votes
1
answer
1.9k
views
1
answers
Answer: A: How to parsing mugsy (.maf) alignment output to RaxML input
... To do that I used biopython, which has a module that is not in the main distribution yet, the module is MafIO (http://biopython.org/wiki/Multiple_Alignment_Format) and with the module AlignIO you can convert from maf to phylip. ...
written 3.7 years ago by rafa.rios.5060

Latest awards to rafa.rios.50

Popular Question 3.3 years ago, created a question with more than 1,000 views. For samtools mpileup Aborted (Core dumped)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1171 users visited in the last hour