User: Mark

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Mark900
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Posts by Mark

<prev • 213 results • page 1 of 22 • next >
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Comment: C: Suggest common programming tasks for biologists who are novice programmers
... I should have added: Not every piece of software you will want to use is installable via package managers. ...
written 9 days ago by Mark900
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Comment: C: kraken2 no longer supported? - NCBI downloads no longer working
... What `h.mon` said is correct. I want to add that downloading from NCBI is very flakey due to all the different network configs. The kraken folks have tried to simplify the process of downloading from NCBI but it's too complicated to fully automate. You should post the error/issue you're having ...
written 16 days ago by Mark900
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Comment: C: Imputing missing genotypes using Beagle
... I might be wrong but I did not see the option `missing`. Also should your REF field contain missing genotypes? I think you have a malformed VCF file, or the `ID` field contains some special character that is causing that error. Can you find `1:78986953` in the vcf file and post it? The other issue I ...
written 16 days ago by Mark900
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Answer: A: How can I download all ncbi genomes files from a given country?
... That's very tricky as I believe NCBI does not force the submitter to include such metadata. Unless there is an organism specific database it's going to require manual curation through reading the literature and linking that metadata back to submission. What organism are you working on? ...
written 16 days ago by Mark900
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Comment: C: Suggest common programming tasks for biologists who are novice programmers
... > Manipulating gene models (get me the locations of all the first introns, or find me single exon genes, or find me transcripts that only differ by a retained intron). What tools do you use for this? I know of R/bioconductor packages designed for this but is there something else? ...
written 17 days ago by Mark900
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Answer: A: Suggest common programming tasks for biologists who are novice programmers
... I have two suggestions. The first: learn to manually install software and their dependancies. Conda and other package managers have made it a breeze to install software, however there are cavets and issues if you rely too much on package managers. The second: Most bio programmers start of writing ...
written 17 days ago by Mark900
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Comment: C: RNA-Seq, HTSeq-Counts, counts are ~1M less compared to the reference research pa
... I would agree but the details are in the devil. Why and when were the reads excluded? Does it affect DE? do the DE counts match? etc etc etc ...
written 6 weeks ago by Mark900
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Comment: C: Pairwise2 Alignment Gap Penalties
... You can define a callback gap function for such cases then: c A callback function returns the gap penalties. Everything is in the documentation. ...
written 6 weeks ago by Mark900
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Comment: C: trimming of fasta file
... I disagree! Sometimes it's easier to just use a gui and get the job done. This is a good example where such usage is perfect. I do this regularly for trimming large MSA aligned to a reference. ...
written 6 weeks ago by Mark900
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Comment: C: Merging bowtie output
... Use the `samtools merge` to merge the bam files. Do not sure `cat` command. ...
written 7 weeks ago by Mark900

Latest awards to Mark

Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: How to perform local realignment around indels without a known vcf file of indel
Teacher 7 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 7 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 12 months ago, created a question with more than 1,000 views. For CNV or Paralog?
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
Teacher 15 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 15 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 15 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 16 months ago, created 100 posts.
Teacher 16 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 16 months ago, voted more than 100 times.
Scholar 16 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 16 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 16 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 16 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Teacher 16 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 16 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Supporter 2.6 years ago, voted at least 25 times.

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