Moderator: Asaf

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Asaf4.6k
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Posts by Asaf

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Comment: C: Looking for phylogenetic python api
... See for instance [ape][1] package in R [1]: http://ape-package.ird.fr/ ...
written 7 days ago by Asaf4.6k
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Comment: C: Looking for phylogenetic python api
... It looks like you have empty sequences, make sure your input is ok. Clustal uses pretty simple algorithms to build the tree, if your desired output is the phylogenetic tree I would recommend to use other algorithms. ...
written 7 days ago by Asaf4.6k
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Answer: A: 16s analysis MySeq PE - analysis of only forward reads?
... If you loose reads when joining paired reads it means that they were problematic to start with, you only disregarded this information. I think you'll get more reliable and accurate results using the paired-end data ...
written 26 days ago by Asaf4.6k
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Comment: C: How to identify if certain recurrent SNPs in a given cancer are associated with
... Sounds like your data is good. Why Fisher? Don't you want to use the actual expression levels for a t-test or Wilcoxon test? ...
written 26 days ago by Asaf4.6k
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Answer: A: How to identify if certain recurrent SNPs in a given cancer are associated with
... You have so much noise in the system, you should take good care or you'll end up with nothing. A few questions you might want to ask yourself: 1. Is all the expression data generated in the same way? Is there a batch effect? 2. Do you have a reference tissue to compare expression to or are you ju ...
written 26 days ago by Asaf4.6k
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Comment: C: Probability of finding a 16S read in 1000 bp fragments
... You should take distance from origin of replication as a factor as well, depending on replication rate. ...
written 27 days ago by Asaf4.6k
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Answer: A: DESeq2 biais when genes are missing from the annotation?
... I'll start from the end: adding unmapped reads will not help with normalization. And for the main question: DESeq2 uses the median value of the ratio between A and B assuming most of the genes have the same expression level. If this assumption holds for your data as well then you're safe using DESe ...
written 29 days ago by Asaf4.6k
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Comment: C: Tools for finding tissue specific gene expression "markers"?
... No, you can download all the data using the Table Browser (tools->table browser) ...
written 4 weeks ago by Asaf4.6k
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Comment: C: Tools for finding tissue specific gene expression "markers"?
... The UCSC genome browser has expression information for human genes, maybe you can download it using table browser and use the data to find the most likely tissue. ...
written 4 weeks ago by Asaf4.6k
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Comment: C: position frequency/weight matrices
... Motif scanning might turn out to be less powerful than you expected. ...
written 4 weeks ago by Asaf4.6k

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Teacher 28 days ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Scholar 28 days 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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Commentator 3 months ago, created a comment with at least 3 up-votes. For C: What to do after an genome assembly?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Scholar 3 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Appreciated 6 months ago, created a post with more than 5 votes. For A: How To Mark Specific Species On The Tree Of Life?
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Commentator 7 months ago, created a comment with at least 3 up-votes. For C: What to do after an genome assembly?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Popular Question 8 months ago, created a question with more than 1,000 views. For Getting transcripts from BAM file with gene names
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Scholar 9 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 13 months ago, created a question with more than 1,000 views. For Counting reads for gene in bacterial genomes
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Scholar 16 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 16 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 16 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 16 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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