User: Phil S.
Phil S. • 660
- Reputation:
- 660
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- Stuttgart, Germany
- Last seen:
- 3 years, 1 month ago
- Joined:
- 5 years, 10 months ago
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Posts by Phil S.
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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 3.4 years ago by
Phil S. • 660
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... awesome thanks, that's enough info I need for a first shot ! (but btw. do you have any reference for that in literature?)
...
written 3.6 years ago by
Phil S. • 660
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... 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 ...
written 3.6 years ago by
Phil S. • 660
• updated
3.6 years ago by
harold.smith.tarheel • 4.4k
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... 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 ...
written 3.7 years ago by
Phil S. • 660
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... usually the sequence used as first input (the one at the very top) is the reference, yes... so you can just change it!
...
written 3.7 years ago by
Phil S. • 660
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Comment:
C: Fasta sequence extraction
... what do you mean by "batch processing"?
...
written 3.7 years ago by
Phil S. • 660
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... 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 3.7 years ago by
Phil S. • 660
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... 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 3.7 years ago by
Phil S. • 660
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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 3.7 years ago by
Phil S. • 660
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... This is your site! And the file you want to download is this one.
HTH
...
written 3.7 years ago by
Phil S. • 660
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3.3 years ago,
created a question with more than 1,000 views.
For reorder contigs given by nucmer
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3.6 years ago,
created a question with more than 1,000 views.
For Go Enrichment From Protein Id
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created a question with more than 1,000 views.
For Go Enrichment From Protein Id
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For C: What is first publication/mention of term RNA-seq
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created a comment with at least 3 up-votes.
For C: DESeq2: can I correct for relatedness when using data from multiplex families?
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For creating rarefaction curves
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For creating rarefaction curves
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For creating rarefaction curves
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For C: DESeq2: can I correct for relatedness when using data from multiplex families?
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