User: Phil S.

gravatar for Phil S.
Phil S.650
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650
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Location:
Stuttgart, Germany
Last seen:
1 year, 9 months ago
Joined:
4 years, 6 months ago
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c********@gmail.com

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Posts by Phil S.

<prev • 176 results • page 1 of 18 • next >
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Comment: C: pair-end, mate-pairs coding
... maybe you can give us some read header from the mp and pe files so we can see how the differences is encoded! ...
written 2.1 years ago by Phil S.650
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Comment: C: How high/low is library construction efficiency?
... awesome thanks, that's enough info I need for a first shot ! (but btw. do you have any reference for that in literature?) ...
written 2.3 years ago by Phil S.650
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How high/low is library construction efficiency?
... Hi guys,   it's more of a wet lab related question but since it have might affected one or another of you I'll try my luck. Does anyone of you have a reference or an idea of how efficient the library preparation (I know it might differ from protocol to protocol significantly) is? Some good estima ...
library sequencing written 2.3 years ago by Phil S.650 • updated 2.3 years ago by harold.smith.tarheel4.1k
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Negative normalized Enrichment Score (NES) in GSEA analysis
... Dear all,   I can't wrap my head around those negative NES scores one should be able to calculate negative NES. But how is this possible?   It is really straight forward to calculate the ES for a given gene set which can, of course be negative depending on the position of the genes in our ranked ...
gsea written 2.3 years ago by Phil S.650
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Comment: C: How can I change the reference genome in a multiple alignment (maf format)
... usually the sequence used as first input (the one at the very top) is the reference, yes... so you can just change it! ...
written 2.4 years ago by Phil S.650
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Comment: C: Fasta sequence extraction
... what do you mean by "batch processing"? ...
written 2.4 years ago by Phil S.650
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Comment: C: Download whole dataset from NCBI Taxonomy
... It contains this:   nodes.dmp --------- This file represents taxonomy nodes. The description for each node includes the following fields: tax_id -- node id in GenBank taxonomy database parent tax_id -- parent node id in GenBank taxonomy database rank -- rank of this node (super ...
written 2.4 years ago by Phil S.650
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Comment: C: How can I change the reference genome in a multiple alignment (maf format)
... If I understand you correctly, you want to change the reference sequence the alignment is made to. So, this would change the whole alignment. So what you can just do is use the sequences you need and calculate a new alignment using cattle as ref.   ...
written 2.4 years ago by Phil S.650
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Comment: C: Fasta sequence extraction
... Here is an awk, one line solution to you problem. awk 'FS="\t" {if(($2==0) && ($3==145) || ($2==256) && ($3 == 289)) print $1}' < foo.file.txt   if this is your file: GCF_000707685.1_2840 0 145 GCF_000706885.1_542 0 150 GCF_000593365.1_489 0 156 GCF_000593345.1_3957 256 289 G ...
written 2.4 years ago by Phil S.650
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Answer: A: Download whole dataset from NCBI Taxonomy
... This is your site! And the file you want to download is this one.   HTH ...
written 2.4 years ago by Phil S.650

Latest awards to Phil S.

Popular Question 23 months ago, created a question with more than 1,000 views. For reorder contigs given by nucmer
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Go Enrichment From Protein Id
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Go Enrichment From Protein Id
Appreciated 2.7 years ago, created a post with more than 5 votes. For C: What is first publication/mention of term RNA-seq
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: DESeq2: can I correct for relatedness when using data from multiplex families?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For creating rarefaction curves
Popular Question 3.0 years ago, created a question with more than 1,000 views. For creating rarefaction curves
Popular Question 3.1 years ago, created a question with more than 1,000 views. For creating rarefaction curves
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: DESeq2: can I correct for relatedness when using data from multiplex families?
Centurion 3.8 years ago, created 100 posts.
Appreciated 4.0 years ago, created a post with more than 5 votes. For C: What is first publication/mention of term RNA-seq
Good Answer 4.0 years ago, created an answer that was upvoted at least 5 times. For C: What is first publication/mention of term RNA-seq
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