User: Macspider

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Macspider3.2k
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Posts by Macspider

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DESeq2 design suggestions: one combined condition, or two separate conditions?
... 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 ...
R mrnaseq design deseq2 rna-seq written 29 days ago by Macspider3.2k • updated 28 days ago by swbarnes28.9k
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
... Otherwise you can also wrap variables in double quotes (e.g. `"${rvs}"`) so that the interpreter is forced to analyze them and render them as text. ...
written 5 weeks ago by Macspider3.2k
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Comment: C: Filtering low quality score bases from BAM file
... As I said in my comment, "it isn't easy (and perhaps not possible) to remove single positions from it". ...
written 5 weeks ago by Macspider3.2k
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
... Try putting the variables within curly brackets (e.g. `${rvs}`) ...
written 5 weeks ago by Macspider3.2k
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
... 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 Macspider3.2k
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
... Using metaspades v3.14 right now myself. Can you edit your question posting the spades command as well? ...
written 5 weeks ago by Macspider3.2k
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Comment: C: Filtering low quality score bases from BAM file
... 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 Macspider3.2k
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Answer: A: Filtering low quality score bases from BAM file
... 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 Macspider3.2k
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Answer: A: python calculation of protein multiple sequence alignment
... 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 Macspider3.2k
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Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
... 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 Macspider3.2k

Latest awards to Macspider

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Converting blastn output to VCF (for SNPs): what is the quickest way?
Popular Question 3 months ago, created a question with more than 1,000 views. For Best way to compare two samples in a VCF file
Popular Question 3 months ago, created a question with more than 1,000 views. For Best way to compare two samples in a VCF file
Popular Question 4 months ago, created a question with more than 1,000 views. For How to retrieve Blast nr database dimensions?
Popular Question 5 months ago, created a question with more than 1,000 views. For HTSeq not counting all the fragments it should count on a gene
Popular Question 9 months ago, created a question with more than 1,000 views. For Why does bcftools call show variants with genotype 0/0 ?
Popular Question 9 months ago, created a question with more than 1,000 views. For HTSeq not counting all the fragments it should count on a gene
Popular Question 12 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Popular Question 12 months ago, created a question with more than 1,000 views. For Insert size selection for RNASeq data: does it make sense?
Scholar 12 months ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Teacher 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
Popular Question 15 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Popular Question 15 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Scholar 15 months ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Popular Question 16 months ago, created a question with more than 1,000 views. 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?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 21 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: How to add tophat and bowtie to the path?
Popular Question 22 months ago, created a question with more than 1,000 views. For DESeq2 proper design setting

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