User: Mark

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Mark800
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Posts by Mark

<prev • 198 results • page 1 of 20 • next >
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Comment: C: How to run SPANDX3.2
... Spandx automatically detects fastq files. This should be your input: ./SPANDx.sh -r k96243 -m yes -a yes `-o` is not needed (it's for specifying the organism name). Have a look on the github page for usage because you seem slightly confused: https://github.com/dsarov/SPANDx If you specify th ...
written 10 weeks ago by Mark800
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Comment: C: Make genes from GTF annotation searchable in IGV
... I think you should pose this question to the IGV developers. It's a good question! ...
written 3 months ago by Mark800
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Comment: C: Make genes from GTF annotation searchable in IGV
... Why do you say it's too large to load without indexing? If your computer has enough ram but IGV is still throwing out an error, you have to increase the allowable memory used by java. You'll have to google but from memory it was annoying but doable. Maybe the solution would be to subset the genome ...
written 3 months ago by Mark800
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Comment: C: Make genes from GTF annotation searchable in IGV
... IGV should happily search tracks: http://software.broadinstitute.org/software/igv/?q=navigate#search You're running it locally or using the web browser? ...
written 3 months ago by Mark800
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Comment: C: kraken2 don't output report files
... you need to reply under this message, not post an answer like you did. ...
written 3 months ago by Mark800
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Comment: C: COG analysis using whole genome data
... The cog database, to my knowledge, has not been updated in a long long time (since 2014). If your organise is not part of the 2014 update, then you will need to manually assign cog categories to the genes. `Prokka` does this for you in an automated fashion. I personally find ontology analysis (inc ...
written 3 months ago by Mark800
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Comment: C: EnhancedVolcano selectLab issue
... thanks for posting the answer! good job on solving it :) ...
written 3 months ago by Mark800
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Comment: C: EnhancedVolcano selectLab issue
... can you post a snippet of your data? ...
written 3 months ago by Mark800
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Comment: C: Detailed process for building snpEff database for NCBI RefSeq genomes?
... You're asking a few questions, and I think the answer is: depends on what you're trying to do, which you haven't explained. I don't think it matters (apart from speed) whether you build a snpeff db for each contig or process them together. I would follow previous examples and process each individual ...
written 3 months ago by Mark800
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Comment: C: kraken2 don't output report files
... what version of kraken2 are you using? ...
written 3 months ago by Mark800

Latest awards to Mark

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to perform local realignment around indels without a known vcf file of indel
Scholar 3 months ago, created an answer that has been accepted. For A: How to perform local realignment around indels without a known vcf file of indel
Popular Question 8 months ago, created a question with more than 1,000 views. For CNV or Paralog?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to perform local realignment around indels without a known vcf file of indel
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to perform local realignment around indels without a known vcf file of indel
Scholar 12 months ago, created an answer that has been accepted. For A: How to perform local realignment around indels without a known vcf file of indel
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to perform local realignment around indels without a known vcf file of indel
Centurion 12 months ago, created 100 posts.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to perform local realignment around indels without a known vcf file of indel
Voter 12 months ago, voted more than 100 times.
Scholar 12 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 13 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 13 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 13 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to perform local realignment around indels without a known vcf file of indel
Scholar 13 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Supporter 2.3 years ago, voted at least 25 times.

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