Moderator: Asaf

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Asaf4.1k
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Posts by Asaf

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Comment: C: Identifying paralogs using phylogenetic tree
... You might want to take a look at: https://www.nature.com/nature/journal/v449/n7158/full/nature06107.html They did this for fungi and were able to track down paralogs, especially after the whole genome duplication event. ...
written 22 hours ago by Asaf4.1k
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Comment: C: Mothur crash issue
... Which version of mothur are you using? ...
written 13 days ago by Asaf4.1k
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Comment: C: Retrieving upstream and downstream intron coordinates
... Bedtools should help ...
written 21 days ago by Asaf4.1k
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Answer: A: Raw expression data is better for FPKM normalised expression profile in RNA seq
... In a nutshell, because you'll be able to apply statistical models to your values. When you normalize to FPKM you lose your ability to do so and end up with less robust statistical tests ...
written 21 days ago by Asaf4.1k
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Answer: A: Development of a tool for NGS
... Write a software that does a lot of small things on fasta or fastq files. Search here for questions like how can I change the header, how to extract etc. In the end you'll have a library that would be very useful. Since it's a course you should put the emphasis on building it correctly rather than ...
written 21 days ago by Asaf4.1k
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Comment: C: Java memory issue in GATK
... Did the specific node had more memory or the cluster in general? If the jobs are not distributed well enough, several jobs find themselves on the same node, exhausting its memory. ...
written 5 weeks ago by Asaf4.1k
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Comment: C: Msc in bioinformatics - MathStatistics as optional courses?
... What is your background? ...
written 5 weeks ago by Asaf4.1k
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Comment: C: Conservation Score Of Amino Acid Positions (2017)
... 1. I'll always prefer an old tool which is still maintained over a new one. 2. You can look for papers citing old tools to see which new tools are out there. ...
written 5 weeks ago by Asaf4.1k
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Comment: C: Incomplete titles in the BLAST output
... With outfmt 6 you can add stitle ...
written 6 weeks ago by Asaf4.1k
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Comment: C: rRNA of E coli in UCSC browser
... They're in the track Genbank ncRNAs, change it to full and search for rRNAs. The names are not the gene names but Blattner numbers (e.g. b0204) ...
written 6 weeks ago by Asaf4.1k

Latest awards to Asaf

Commentator 5 days ago, created a comment with at least 3 up-votes. For C: What to do after an genome assembly?
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Popular Question 21 days ago, created a question with more than 1,000 views. For Getting transcripts from BAM file with gene names
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Getting transcripts from BAM file with gene names
Scholar 9 weeks ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Popular Question 5 months ago, created a question with more than 1,000 views. For Counting reads for gene in bacterial genomes
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Popular Question 7 months ago, created a question with more than 1,000 views. For What Do You Waste Your Time On
Scholar 8 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 8 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 8 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 8 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 8 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 8 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Scholar 9 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Great Question 12 months ago, created a question with more than 5,000 views. For What Do You Waste Your Time On
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Popular Question 14 months ago, created a question with more than 1,000 views. For What Do You Waste Your Time On
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms

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