User: Leeandroid v2.9

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Universitat Politècnica de València
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Posts by Leeandroid v2.9

<prev • 8 results • page 1 of 1 • next >
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Change sample names in vcf
... Hi everyone. I want to simplify the names of the samples of a VCF file by removing the suffix that was added during sequenciation but i am not being successful. Right now my samples are named like this: 123_4:A7TT6AKXX:1:1000000001 or ABC100:A7TT6AKXX:1:1000000001 In the first case I want to kee ...
vcf sample name written 13 hours ago by Leeandroid v2.920 • updated 13 hours ago by MAPK1.0k
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Answer: A: Clustering program based on NJ phylogeny
... Check http://evolution.genetics.washington.edu/phylip.html. ...
written 23 days ago by Leeandroid v2.920
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Comment: C: Filter VCF with txt
... Thank you, Alex. It worked! ...
written 24 days ago by Leeandroid v2.920
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Comment: C: Filter VCF with txt
... Hi Alex, thanks for your reply. It was really helpful! I was able to filter the desired snp's but now I have an output file without the headers (## lines). How can I prevent that from happening? I ran the command: grep -e -F -f id.txt my.vcf > filtered.vcf Thanks. ...
written 24 days ago by Leeandroid v2.920
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Filter VCF with txt
... Hi everyone. I'm trying to filter a vcf with a txt that has only the ID column but I keep getting the following error message: *[E::bcf_sr_regions_init] Could not parse the file list.txt, using the columns 1,2[,-1] Failed to read the targets: ^list.txt* I've been using the following command: *bcft ...
vcf snp filtering written 24 days ago by Leeandroid v2.920 • updated 24 days ago by Alex Reynolds21k
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Answer: A: Unable to install SNPhylo in ubuntu
... You should install them by opening R and paste (one at a time) the following: > install.packages("getopt", repos="http://cran.r-project.org") > install.packages("phangorn", repos="http://cran.r-project.org") > source("http://bioconductor.org/biocLite.R") > biocLite("gdsfmt") > bi ...
written 25 days ago by Leeandroid v2.920
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Answer: A: Unable to install SNPhylo in ubuntu
... I don't know if I fully understand what you mean but I believe that the problem is the R installation. Can you run R? If so, when installing SNPhylo you just have to give the full path to the R binary file, usually at /bin directory. Hope it helps. ...
written 27 days ago by Leeandroid v2.920
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Comment: C: Multi-Sample Vcf To Phylogenetic Tree.
... Greetings. My goal is to biuld a phylogenetic tree (bootstrapped) based on the VCF file have. I recently started to learn bioinformatics, and how to use some of the avaiable tools. After browsing for a while I found SNPhylo that seemed to fit. Everything went fine untill I got this error message: ...
written 5 months ago by Leeandroid v2.920

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