User: rob.costa1234

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rob.costa1234150
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Posts by rob.costa1234

<prev • 107 results • page 1 of 11 • next >
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MetaCore Interactome enrichment tool
... I am trying to find where (GUI or command line) can I run MetaCore Interactome enrichment tool published in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489533/ and cited in several publications such as https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133374/#bib2 ...
tool written 15 days ago by rob.costa1234150 • updated 15 days ago by h.mon13k
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Comment: C: Sequencing with 10X genomics
... there is lot of variation in reads per cell, some go upto 100K to several millions of reads. That is the major cause of confusion. I will write to 10X ...
written 5 weeks ago by rob.costa1234150
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Sequencing with 10X genomics
... I am planning to do single cell RNA-seq with 10X genomic platform. I was wondering if there are any rules to select how many cells I should use and how many reads per cell will be optimal. I have looked into 10x web page (https://support.10xgenomics.com/single-cell-gene-expression/sequencing/doc/s ...
rna-seq written 5 weeks ago by rob.costa1234150
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STAR aligned reads minimum maping quality
... I aligned RNAseq data with GRCH 37 and wonder what cut off of read quality is generally used when we perform downstream analysis. I know in HISAT2 generally read quality >20 is considered. I could not find any general rule of quality cutoff in STAR. Any suggestion? ...
rna-seq written 6 weeks ago by rob.costa1234150 • updated 6 weeks ago by caggtaagtat180
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plotting an expression data in heat map/ hierarchical clustering
... I have an RNAseq data expression matrix 200 rows and 12 columns. I want to show as gradient in expression profiles using either HC or simple heat map. The experiment is to show that with treatment certain genes are upregulated as compared to vector vs expressed gene, while with mutant this expressio ...
rna-seq written 6 weeks ago by rob.costa1234150
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RNAseq analysis Deseq
... I performed RNA seq analysis using Deseq2 (three replicates, 4 grps). However in each two grp comparison FDRp<0.05 gives me > 10,000 genes. I can increase the p value to 0.01 but wonder do we get that many differentially expressed genes with Deseq. I would have expected 200-250 genes in each t ...
rna-seq written 7 weeks ago by rob.costa1234150 • updated 7 weeks ago by seidel6.5k
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database of genes
... I am looking for a list of all autophagy and lysosome associated genes. Is there a database where i can find list of such genes Thanks ...
database written 8 weeks ago by rob.costa1234150
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Sc-RNA seq patients
... How many technical replicates if any should be good for patient based tissue's scRNAseq. Do we really need technical replicate? ...
rna-seq written 8 weeks ago by rob.costa1234150
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Question about Amazon cloud computing for sequencing analysis
... I am planning to get subscription of Amazon cloud for deploying software and allow other users to run their analysis using the deployed tool. Does any one has any experience working with Amazon and if collaborator has to run analysis do they need to pay separate subscription. Any pointer will be gr ...
sequencing written 8 weeks ago by rob.costa1234150
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gene expression database for quary a gene
... Is there a gene expression (RNAseq or array) database that can be be queried for expression level of a particular gene in specific cancer? Thanks ...
rna-seq written 8 weeks ago by rob.costa1234150 • updated 8 weeks ago by Rahul Sharma540

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