Moderator: 5heikki

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5heikki8.4k
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Posts by 5heikki

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Answer: A: Calculating relative abundance of taxonomies from BLAST output
... https://www.biostars.org/p/144569/ ...
written 4 weeks ago by 5heikki8.4k
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Comment: C: Rename fasta headers from CSV
... Do the fasta files have linebreaks in seqs? If not, then perhaps e.g. join -1 1 -2 1 -t $'\t' \ <(sed 's/,/\t/' file.csv | sort -k1,1) \ <(paste - - //' | sort -k1,1) \ | awk 'BEGIN{FS="\t"}{print ">"$2"_"$3"\n"$4}' ...
written 8 weeks ago by 5heikki8.4k
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Comment: C: intersection for several file
... If by intersection OP means that the line has to be in every file, then the above does not work.. However (the same than JC's answer really).. cat file* | sort | uniq -c | awk '{if($1==6){print $2}}' ...
written 8 weeks ago by 5heikki8.4k
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Comment: C: What does it mean if a gene is not found in an assembly?
... Extract your gene of interest +/- 10k bp region from a large number of reference genomes of your species. Do they align nicely? If yes, that region is conserved across your species. Now map your reads against this region. In case you see something like "|||||||||||||.....|||||||||||||||" (with pipes ...
written 10 weeks ago by 5heikki8.4k
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Comment: C: What does it mean if a gene is not found in an assembly?
... Another thing you can do is to pick a reference genome that is the closest to your sequenced genome. Then you map the reads from your genome on the reference genome and see what is missing (other than your gene of interest that is).. ...
written 10 weeks ago by 5heikki8.4k
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Comment: C: What does it mean if a gene is not found in an assembly?
... I haven't done any wetlab stuff for a very long time, but IMO starting from a cell culture, it would take extraordinary skill to somehow manage to extract the DNA covering just 50% of some prokaryotic genome.. ...
written 10 weeks ago by 5heikki8.4k
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Comment: C: What does it mean if a gene is not found in an assembly?
... I don't know about eukaryote genomes, but I disagree with that you can have high coverage, few contig, high N50 prokaryote genome assembly (you defined bacteria in OP) and still miss a considerable part of the genome. "Hundreds of genes" is less than 1% of all genes in the context of your typical ma ...
written 10 weeks ago by 5heikki8.4k
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Comment: C: What does it mean if a gene is not found in an assembly?
... IMO if you have +20X coverage for your contigs and the assembly is of decent quality (~100 contigs or less, N50 > 50k) and blastn returns nothing, then conclusion is that the sequenced organism does not have that specific gene ...
written 10 weeks ago by 5heikki8.4k
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Answer: A: FastQC results interpretation
... Try [FASTQE][1] [1]: https://fastqe.com/ ...
written 11 weeks ago by 5heikki8.4k
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Comment: C: phylogenetic analysis of pathogenic bacteria
... Why do people ask questions without providing any background information whatsoever? ...
written 3 months ago by 5heikki8.4k

Latest awards to 5heikki

Teacher 9 days ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Script for extracting data from a tab-delimited file
Scholar 4 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 4 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 4 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 4 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Scholar 6 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 7 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
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Popular Question 7 months ago, created a question with more than 1,000 views. For Print all rows that are in specified value range based on specific column as pairs
Scholar 8 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Popular Question 8 months ago, created a question with more than 1,000 views. For #saveNCBI - it's a joke, right?
Popular Question 9 months ago, created a question with more than 1,000 views. For #saveNCBI - it's a joke, right?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Script for extracting data from a tab-delimited file
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?

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