Moderator: Asaf

gravatar for Asaf
Asaf4.0k
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4,020
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Location:
Israel
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Google Scholar Page
Last seen:
7 hours ago
Joined:
5 years, 11 months ago
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Posts by Asaf

<prev • 445 results • page 1 of 45 • next >
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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 10 days ago by Asaf4.0k
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Comment: C: Msc in bioinformatics - MathStatistics as optional courses?
... What is your background? ...
written 10 days ago by Asaf4.0k
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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 10 days ago by Asaf4.0k
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Comment: C: Incomplete titles in the BLAST output
... With outfmt 6 you can add stitle ...
written 12 days ago by Asaf4.0k
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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 17 days ago by Asaf4.0k
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Answer: A: De novo bacteria transcriptome assembly options
... It's relatively easy (compared to eukaryotes). You can use software for DNA assembly but make sure it doesn't assume even coverage. rnaSPAdes or metaSPAdes should work. ...
written 18 days ago by Asaf4.0k
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Comment: C: Finding Batch effects in RNAseq data
... You can include batch effect in your model in DESeq2 as well ...
written 20 days ago by Asaf4.0k
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Comment: C: Batch conservation analysis
... The easiest way would probably be to convert maf to vcf and then use vcftools to intersect it with bed files. See this thread: https://www.biostars.org/p/142944/ for conversion option. ...
written 24 days ago by Asaf4.0k
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Comment: C: Curiosity about DESeq2
... Probably normalization ...
written 25 days ago by Asaf4.0k
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Comment: C: cuffnorm got high fpkm TCONS but few read
... I didn't understand your question completely but what you say makes sense. Short genes with few reads should have higher fpkm than long genes with the same number of reads ...
written 26 days ago by Asaf4.0k

Latest awards to Asaf

Popular Question 3 days ago, created a question with more than 1,000 views. For Getting transcripts from BAM file with gene names
Scholar 5 weeks ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 6 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 4 months ago, created a question with more than 1,000 views. For Counting reads for gene in bacterial genomes
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Popular Question 6 months ago, created a question with more than 1,000 views. For What Do You Waste Your Time On
Scholar 7 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 7 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 7 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 7 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 7 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 7 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
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
Teacher 8 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
Great Question 11 months ago, created a question with more than 5,000 views. For What Do You Waste Your Time On
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Popular Question 13 months ago, created a question with more than 1,000 views. For What Do You Waste Your Time On
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: What to do after an genome assembly?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Scholar 19 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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