User: onspotproductions

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Posts by onspotproductions

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Comment: C: High p-values generated from CuffDiff
... The tools were much older at the time and even different dispersion method doesn't make a difference. ...
written 22 months ago by onspotproductions120
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Comment: C: High p-values generated from CuffDiff
... I know there were no replicates as we are using the exact same data. I will have to try la different dispersion method, but unfortunately we have been unable to obtain the.info file. ...
written 22 months ago by onspotproductions120
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High p-values generated from CuffDiff
... I am doing differential expression analysis on two samples, control and over-expression vector. I am using cuffdiff directly with the gtf file from the human genome as we are only interested in gene expression changes and not transcript level changes. Previously, some analysis was done on the same r ...
differential cufflinks rna-seq expression written 22 months ago by onspotproductions120 • updated 22 months ago by Satyajeet Khare1.3k
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Comment: C: Tool to identify group pair distance & other metrics from FASTQ files
... Yes, group pairs distance is the maximum length expected between fragment pairs. These are parameters for Trinity. ...
written 22 months ago by onspotproductions120
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Tool to identify group pair distance & other metrics from FASTQ files
... I am looking for a tool or pipeline to identify metrics from FASTQ data such as group pairs distance. I would also like to have other metrics like read distribution. ...
fastq metrics rna-seq written 22 months ago by onspotproductions120 • updated 22 months ago by bongok40
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Answer: A: From cuffmerge to cuffdiff: What input for cuffdiff?
... You need to merge all your cufflinks assemblies into a single gtf file using cuffmerge. Both conditions will be contained in a single file. You can then use this within cuffdiff and your original BAM files to test for your conditions. ...
written 2.3 years ago by onspotproductions120
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generating CLS file for GSEA from Cuffdiff output
... I have differential expression data generated from cuffdiff that we would like to perform GSEA & GSVA on. I am unsure how to generate a CLS file for use with either of these toolsets. I plan to uses databases from msigDB and gseapy. ...
differential expression rna-seq gsea written 2.4 years ago by onspotproductions120 • updated 2.1 years ago by BioNinja0
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Merging MISO exon-centric output values according to gene
... I have some data obtained through MISO that has been annotated to contain gene symbols. We used the exon-centric method and would like to find a tool to combine the output diff/bayes values according to gene name. Essentially, what I have been asked to do is create a single value that ells which gen ...
bed splicing miso rna-seq written 2.4 years ago by onspotproductions120
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Comment: C: Methods to identify ORF from de novo assembly
... That is an interesting thought and yes we used transcripts. I will have to try that on one of the sequences of better known characterization. It may also be worth attempting to regenerate the assembly using another assembler and compare the output. ...
written 2.5 years ago by onspotproductions120
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Methods to identify ORF from de novo assembly
... I have recently completed a de novo assembly for an organism whose genome is currently unknown. We are working to classify all the sequences, but would like to decode the ORFs so we can tie our data to data from MS. I have previosuly attempted to use transdecoder w/ homology search and emboss tools ...
assembly rna-seq blast written 2.5 years ago by onspotproductions120

Latest awards to onspotproductions

Popular Question 2.0 years ago, created a question with more than 1,000 views. For Gene ID mapping of Ensembl IDs
Scholar 2.3 years ago, created an answer that has been accepted. For A: From cuffmerge to cuffdiff: What input for cuffdiff?

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