User: ricfoz

gravatar for ricfoz
ricfoz20
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Location:
National School of Antropology and History, Mexico city, Mexico
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1 week, 2 days ago
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9 months ago
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r*****@hotmail.com

Posts by ricfoz

<prev • 53 results • page 1 of 6 • next >
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How many works can clustalw can support at the same time?
... Hello everyone I am trying to align several fasta files using clustalw through a remote server in my university. The jobs are quite time consuming, and i am wondering if it is possible to run three jobs at the same time. I know i can, i just want to know if it is recommended, or if i just have to w ...
multiple jobs clustalw written 10 weeks ago by ricfoz20
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Comment: C: Issue while sorting a file
... .. I also ran the gdb command you suggested, it didn´t give any error message, it just worked as usually, outputting what the program is doing in a verbrose manner. but all ran smoothly. ...
written 11 weeks ago by ricfoz20
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Comment: C: Issue while sorting a file
... Thank you... I ran the pipe with wc -l as you suggested. The number of lines it tells the files have are the same !, i think that means that the info may be the same? It is very weird, still, i don't think there is any trouble with the compression with my samtools, since i have run the tool on othe ...
written 11 weeks ago by ricfoz20
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Issue while sorting a file
... hello everyone I am working with some bam files, and trying to retrieve a fasta sequence from them. I have sorted my workflow, but i have an inquiry since the size of the files doesn't seem to match, i describe my issue as follows: My original bam file has 2Gb size, when i sort it in order to ret ...
inconsistency trouble sort written 11 weeks ago by ricfoz20 • updated 11 weeks ago by drkennetz340
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looking for a tree viewer useful for .con.tre file outputted from MrBayes
... Hello community, I have run a Marcov Chain Monte Carlo analysis usin MrBayes. It run succesfuly and outputted (besides a few other files) a consensus .con.tre file which i was able to print in a tree viewer called FigTree-v1.4.3; it was pretty useful, but i have some branches which are short, and o ...
mrbayes viewer tree treeviewer written 3 months ago by ricfoz20 • updated 3 months ago by Kevin Blighe25k
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Comment: C: Filter low quality reads in bam files
... It might be a terrible idea in some cases, but when working with ancient DNA, which might have sequencing errors due to oxidative and hidrolytic damage as to contamination, you might want to trim bases below certain quality (usually <30), anyways, i just write this in order to enrich the discussi ...
written 4 months ago by ricfoz20
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Comment: C: error while using " samtools mpileup " function
... Hey, i have tried the code you provide, and i see what you mean .. in the middle of those commands, i need to add in the header the information "SRC-5-alex4__MA167snp" into the header, before reheadering the file, so all the read groups have the tag and can be piled up by the "mpileup" command. Any ...
written 6 months ago by ricfoz20
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Comment: C: error while using " samtools mpileup " function
... Hey there Devon. That makes sense (of course, since you know what you are talking about), i visually checked my used bam files, and the problem is after the alignment, say, all of the ones who work well have 10 information columns after the alignment section, these columns are the next ones in a tr ...
written 6 months ago by ricfoz20
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error while using " samtools mpileup " function
... Hello everyone, I am trying to run a workflow from a complete genome .bam file all the way to the consensus of a fasta sequence from the .vcf file constructed through the process. After sorting, indexing, and retreiving a .bam file with the genic strand i wish to work with, i need to run > sa ...
headers read_group samtools mpileup error written 6 months ago by ricfoz20 • updated 6 months ago by Devon Ryan82k
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Comment: C: Unable to install bwa-0.7.17 on ubuntu 10.06 virtualbox machine.
... i thought that myself, but i haven't been able either. Unless i have been getting things wrong. Is bioconda the same, or a dependence of Anaconda package? , i know i can set a conda environment through Anaconda to install packages, but that hasn't worked, but i should ask you if bioconda is the same ...
written 7 months ago by ricfoz20

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