User: Macspider
Macspider • 3.2k
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Posts by Macspider
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... Hi guys,
During my PhD and early postdoc I have performed a differential gene expression analysis more than once. In each case, I have used the classic workflow including htseq + DESeq2.
I know how it works, I know the pitfalls, I know the possible biases, but one theoretical question still stand ...
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... Otherwise you can also wrap variables in double quotes (e.g. `"${rvs}"`) so that the interpreter is forced to analyze them and render them as text. ...
written 5 weeks ago by
Macspider • 3.2k
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... As I said in my comment, "it isn't easy (and perhaps not possible) to remove single positions from it". ...
written 5 weeks ago by
Macspider • 3.2k
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... Try putting the variables within curly brackets (e.g. `${rvs}`) ...
written 5 weeks ago by
Macspider • 3.2k
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... Is all of this inside a shell script? If so, could you try to execute it from the command line and see if it works? Sometimes variables within shell scripts require special handling. ...
written 5 weeks ago by
Macspider • 3.2k
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... Using metaspades v3.14 right now myself. Can you edit your question posting the spades command as well? ...
written 5 weeks ago by
Macspider • 3.2k
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... Just a suggestion: `MarkDuplicate` and `AddReadGroups` are not "steps", but functions of a program (I guess it's picard). Not everyone removes duplicates, and most of the times you don't need read groups unless you're using GATK. This suggests me that you're using someone else's variant calling pipe ...
written 5 weeks ago by
Macspider • 3.2k
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... Filtering read-mapping records is usually done with tools like **samtools view**:
http://www.htslib.org/doc/samtools-view.html
Among the options, there is `-q ` which discards reads with mapping quality below `N`. However, it isn't easy (and perhaps not possible) to remove single positions from it ...
written 5 weeks ago by
Macspider • 3.2k
4
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... I think what you're looking for is contained in `scipy.spatial.distance`:
https://docs.scipy.org/doc/scipy/reference/spatial.distance.html
Among these measurements, I would suggest you to have a look at the Jaccard distance. It fits your requirement of the [0,1] range, and it's pretty easy to calc ...
written 5 weeks ago by
Macspider • 3.2k
0
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... Improving the assembly and generating a reference metatranscriptome is what we're set out to do in the next 12 months :) ...
written 5 weeks ago by
Macspider • 3.2k
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For A: How to convert .bed file to .juncs file using Tophat?
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5 weeks ago,
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7 weeks ago,
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For A: How to convert .bed file to .juncs file using Tophat?
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10 weeks ago,
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12 months ago,
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12 months ago,
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For Insert size selection for RNASeq data: does it make sense?
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12 months ago,
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For A: How to convert .bed file to .juncs file using Tophat?
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12 months ago,
created an answer with at least 3 up-votes.
For A: How to convert .bed file to .juncs file using Tophat?
Scholar
12 months ago,
created an answer that has been accepted.
For A: How to convert .bed file to .juncs file using Tophat?
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Quality, MQ0F, other parameters for proper VCF filtering
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15 months ago,
created a question with more than 1,000 views.
For Quality, MQ0F, other parameters for proper VCF filtering
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15 months ago,
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For Quality, MQ0F, other parameters for proper VCF filtering
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15 months ago,
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For A: How to convert .bed file to .juncs file using Tophat?
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16 months ago,
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For Quality, MQ0F, other parameters for proper VCF filtering
Great Question
19 months ago,
created a question with more than 5,000 views.
For Remove duplicates from reads: best practices?
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21 months ago,
created an answer with at least 3 up-votes.
For A: How to convert .bed file to .juncs file using Tophat?
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21 months ago,
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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For C: How to add tophat and bowtie to the path?
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22 months ago,
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For DESeq2 proper design setting
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