User: beegrackle

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beegrackle90
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United States
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3 months, 1 week ago
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3 years, 1 month ago
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Posts by beegrackle

<prev • 10 results • page 1 of 1 • next >
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Chloroplast 16S sequences - any fun to be had?
... I am working with some 16S sequences (V4 region) from soils. I am looking at bacterial diversity and so of course removed chloroplast sequences, but I took a look at them and I am very curious about some of the patterns I am seeing in the phylogenetic tree in correlation with environmental variables ...
16s taxonomy sequencing written 3 months ago by beegrackle90 • updated 3 months ago by 5heikki7.3k
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Comment: C: cutadapt and paired-end reads when you don't know your adapter sequences...
... Unfortunately - no. Instead all my overrepresented sequences are my forward primer (or reverse primer) and a following 10-bp sequence. Which is rather dodgy, I admit. ...
written 14 months ago by beegrackle90
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Comment: C: cutadapt and paired-end reads when you don't know your adapter sequences...
... Thanks - that worked out *really* well! ...
written 14 months ago by beegrackle90
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cutadapt and paired-end reads when you don't know your adapter sequences...
... Hi all, I have some amplicon sequencing data from a company that has been endlessly frustrating to work with...it is a long story, but they basically dumped my sequencing data on a server without any information about what the adapter sequences were, etc. and then skedaddled. So I went and looked a ...
next-gen sequencing written 14 months ago by beegrackle90 • updated 14 months ago by YaGalbi1.3k
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How to get pfam seed sequence taxonomy info?
... Is there an easy(ish) way to get the taxonomy information for pfam seed sequences? For the life of me I cannot figure out any other way to do it than blasting each seed sequence and getting the top hit off of ncbi, which is ridiculous because pfam links to ncbi and vice-versa. Since pfam has the opt ...
ncbi taxonomy blast pfam written 3.0 years ago by beegrackle90 • updated 3.0 years ago by Biostar ♦♦ 20
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Exporting trees from ITOL - legend not displaying correctly
... I am in love with ITOL! However, when I try to export a tree, all the legends are wayyyy up in the righthand corner, tiny as can be. Changing format, font size, tree scale factor...nothing seems to help and usually makes it worse. Anyone have experience with this? ...
itol phylogenetic tree written 3.0 years ago by beegrackle90 • updated 2.9 years ago by Biostar ♦♦ 20
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Comment: C: Bio.Entrez - Get virus host name using NCBI Taxonomy db
... Thanks Neilfws, especially for the regex bit :) ...
written 3.1 years ago by beegrackle90
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Answer: A: Principal component analysis in R on expression data
... Your problem might be that the R default palette only has 8 colors (see here), and so R is just recycling through those colors. You could try manually entering in the colors = col=c("red", "green", etc up to 17)[cols] , or use RColorBrewer (the link has some examples of that) to generate a palette w ...
written 3.1 years ago by beegrackle90
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Answer: A: Parse the Xml response from Entrez Db=bioproject Using Biopython eFetch
... Hi Prasad: I was working on the same problem two weeks ago; I finally gave up and used Beautiful Soup to parse the xml results by going through, studying the xmls and the different parent nodes of the child nodes I want, and checking that the full path for each item I wanted exists before I put it ...
written 3.1 years ago by beegrackle90
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Bio.Entrez - Get virus host name using NCBI Taxonomy db
... I'm trying to create a fasta file with all the viral sequences for a particular gene, with taxonomy information in the record description. So far so good, except that while I can see the general host information on the taxonomy page of each virus (For example this virus: http://www.ncbi.nlm.nih.gov/ ...
ncbi entrez biopython virus written 3.1 years ago by beegrackle90 • updated 2.8 years ago by howcouldyouforgetthisusername0

Latest awards to beegrackle

Popular Question 14 months ago, created a question with more than 1,000 views. For How to get pfam seed sequence taxonomy info?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Bio.Entrez - Get virus host name using NCBI Taxonomy db
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Principal component analysis in R on expression data
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Principal component analysis in R on expression data
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Principal component analysis in R on expression data
Scholar 3.1 years ago, created an answer that has been accepted. For A: Principal component analysis in R on expression data

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