User: ricfoz

gravatar for ricfoz
ricfoz20
Reputation:
20
Status:
New User
Location:
National School of Antropology and History, Mexico city, Mexico
Last seen:
2 weeks, 3 days ago
Joined:
6 months, 1 week ago
Email:
r*****@hotmail.com

Posts by ricfoz

<prev • 49 results • page 1 of 5 • next >
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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 20 days ago by ricfoz20 • updated 18 days ago by Kevin Blighe19k
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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 9 weeks 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 3 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 3 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 3 months ago by ricfoz20 • updated 3 months ago by Devon Ryan79k
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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 4 months ago by ricfoz20
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Comment: C: Unable to install bwa-0.7.17 on ubuntu 10.06 virtualbox machine.
... As far as i know, i am on a 64 bit host. OS Win7, my virtual machine is running ubuntu 16.04, yet i have architecture i686, which i have read is supposed to be 32 bit. i have printed my cpu info running > $ lscpu the pertinent info reads as follows: > Architecture: i686 CPU op-mod ...
written 4 months ago by ricfoz20
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Unable to install bwa-0.7.17 on ubuntu 10.06 virtualbox machine.
... hello all, i am trying to install bwa in my ubuntu guest virtual-machine. i have already downloaded, extracted .bz2 file, untared the resulting file, and i am standing in the bwa-0.7.17 folder. as i type make i receive the next set of errors: (sorry for the length, i just wanted to share the compl ...
install error intall error trouble bwa written 4 months ago by ricfoz20 • updated 4 months ago by colindaven640
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Answer: A: Opinion on Quality basecall threshold to use
... Alright, i've been searching for further information about what you post, and i have filtered my files to get a consensus using only the variants above QUAL 30 ... Would you say 30 is a fair number to filter on, or should i raise the standard? Cheers ...
written 4 months ago by ricfoz20
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Comment: C: Opinion on Quality basecall threshold to use
... Alright, and how is the meassure of the quality of the variant call in vcfs expressed?, in some cases i haven't got acces to fastq files, although it is possible to convert bams to fastq as far as i know. Maybe this conversion allows to see the basecall quality when comming from a bam ? ...
written 5 months ago by ricfoz20

Latest awards to ricfoz

Scholar 6 months ago, created an answer that has been accepted. For C: getting a consense one header .fasta file from a genic region, from .bam templat

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