Moderator: Asaf

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Asaf4.1k
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Posts by Asaf

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Comment: C: Best way to address different batches of RNA-seq
... What was different between the two batches? In addition, as said above you shouldn't use RPKM, use statistics as in DESeq2 ...
written 23 days ago by Asaf4.1k
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Answer: A: Gene abundance profile from metagenomics data
... I'm not aware of such a tool. You can try and classify your genes using interpro domains, MetaCyc/KEGG orthology groups etc. Depending on your depth of sequencing and sample complexity I would consider reference-based counting (i.e. mapping the reads to a reference using blastx) instead of assembly ...
written 23 days ago by Asaf4.1k
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Comment: C: Normalization methods for metagenomics WGS data (not 16S data)
... DESeq2 normalization process assumes that most of the entities are the same in all of the samples. If you think that this assumption applies then you're good to go with DESeq2, you can go forward and do the entire analysis with it. If, however, this is not the case and the population is completely d ...
written 8 weeks ago by Asaf4.1k
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Comment: C: Normalization methods for metagenomics WGS data (not 16S data)
... If you have a table with read counts then DESeq2 should work, the main issue here is what reference to use. ...
written 8 weeks ago by Asaf4.1k
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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 8 weeks ago by Asaf4.1k
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Comment: C: Mothur crash issue
... Which version of mothur are you using? ...
written 10 weeks ago by Asaf4.1k
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Comment: C: Retrieving upstream and downstream intron coordinates
... Bedtools should help ...
written 11 weeks 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 11 weeks 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 11 weeks 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 3 months ago by Asaf4.1k

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