User: leeandroid

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leeandroid20
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New User
Location:
Spain/Valencia/UPV
Last seen:
4 hours ago
Joined:
8 months ago
Email:
l************@gmail.com

Posts by leeandroid

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Change sample names in vcf
... It works, cpad0112! Thank you for your precious help. ...
written 11 weeks ago by leeandroid20
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Comment: C: Change sample names in vcf
... Added header but not sure if in the right format. I'll try your solution and post if it worked. Thank you! ...
written 11 weeks ago by leeandroid20
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Comment: A: Change sample names in vcf
... Thank you all for replying! Seems that I failed to explain myself on the original post. The goal is to change the names of my samples like this: 123_4:A7TT6AKXX:1:1000000001 > 123 ABC100:A7TT6AKXX:1:1000000001 > ABC100 Eventually I was able to change them using bcftools reheader* - like Pie ...
written 12 weeks ago by leeandroid20
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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 ...
vcf sample name written 12 weeks ago by leeandroid20
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Answer: A: Clustering program based on NJ phylogeny
... Check http://evolution.genetics.washington.edu/phylip.html. ...
written 3 months ago by leeandroid20
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Comment: C: Filter VCF with txt
... Thank you, Alex. It worked! ...
written 3 months ago by leeandroid20
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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 3 months ago by leeandroid20
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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 3 months ago by leeandroid20 • updated 3 months ago by Alex Reynolds22k
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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 3 months ago by leeandroid20
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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 3 months ago by leeandroid20

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