Moderator: Asaf

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Asaf6.1k
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Posts by Asaf

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Comment: C: including batch in design~
... The name of the batch (like sequencing lane ID for instance) each library was prepared and sequenced in ...
written 2 minutes ago by Asaf6.1k
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Comment: C: including batch in design~
... `batch` should a=be a column in the `samples` data.frame you provided ...
written 9 hours ago by Asaf6.1k
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Comment: C: PCA-based clustering gene expression data
... How many dimensions of the PCA are you using for clustering? ...
written 7 days ago by Asaf6.1k
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Comment: C: Establishing a metagenomics lab/hardware requirements
... I don't know, you might want to find someone that established such an infrastructure lately. Do you have any support from your institute? A computer cluster, a backup system, most institutions have some of those things. You might want to reach out to the CS department if you have such or ask around ...
written 7 days ago by Asaf6.1k
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Comment: C: Establishing a metagenomics lab/hardware requirements
... It's not just storage capacity, it's also its speed. ...
written 7 days ago by Asaf6.1k
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Comment: C: InterProScan and HMMER - different results
... My guess is that the multiple hypotheses correction is different, probably interproscan scans more profiles and has a more profound correction. Can you validate the correspondence between the e-values? Are you loosing the high e-value results? ...
written 13 days ago by Asaf6.1k
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Comment: C: Batch effect control in GWAS data.
... I would start by cleaning the data using a procedure like in here: https://kbroman.org/qtl2/assets/vignettes/do_diagnostics.html especially the "Array intensity" part. To even better make the data comparable I would select an unrelated evenly spaced list of markers which is in a bit of lower resolut ...
written 18 days ago by Asaf6.1k
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Comment: C: Batch effect control in GWAS data.
... > i have removed all SNP`s which have p < 0.05 when one platform is used > as case and the other one as control So you remove all the peaks? ...
written 18 days ago by Asaf6.1k
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Comment: C: Process RNA-Seq Data with specific sequences / not whole reference genome
... BAM file shouldn't contain gene ids just chromosomes and positions. The genes (or features) are defined in the gff file ...
written 20 days ago by Asaf6.1k
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Comment: C: Process RNA-Seq Data with specific sequences / not whole reference genome
... It's pretty straightforward, map the fastq files to the genome, run htseq-count and analyze only the features (genes?) of interest. ...
written 20 days ago by Asaf6.1k

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Scholar 7 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 11 weeks ago, created a comment with at least 3 up-votes. For C: Normalization in RNA-seq
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Scholar 3 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 3 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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Commentator 5 months ago, created a comment with at least 3 up-votes. For C: What to do after an genome assembly?
Scholar 5 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: How To Mark Specific Species On The Tree Of Life?
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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 17 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 20 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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