User: bioyas

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bioyas0
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Posts by bioyas

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Comment: C: getting 0 counts using hisat2 and feature_count pipeline
... Thanks! I checked that. The Chromosome names were different. I could get the counts. ...
written 27 days ago by bioyas0
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Comment: C: getting 0 counts using hisat2 and feature_count pipeline
... I checked the Gene Id in the gif file and gene ids in one of the feature counts output. they seem to be the same.![][1] [1]: https://cdn1.imggmi.com/uploads/2020/1/24/2155fb8a7d22aea505aacf542f7dcb1a-full.png ...
written 27 days ago by bioyas0
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getting 0 counts using hisat2 and feature_count pipeline
... Hello everyone, I am new to bioinformatics and I am trying to extract gene count using hisat2 pipeline and feature count. But I am getting 0 counts for all genes. Here is the steps that I am taking: 1. I have generated the genome index files using hisat2_build_index command. 2. Then I aligned ...
count featurecounts rna-seq hisat2 written 27 days ago by bioyas0 • updated 27 days ago by swbarnes27.4k
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Comment: C: How to get the gene expression matrix from GEO while getGEO returns 0 features?
... Thanks for your response. On the GEO page I can see that there is a file "GSE104075_RAW.tar" that contains the bed files. I have unzipped them and I see the files with ".bed" and ".bedGraph". Do you think I can use this files to get the gene expression data? Do you think I can convert bed files t ...
written 7 months ago by bioyas0
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How to get the gene expression matrix from GEO while getGEO returns 0 features?
... Hi, I would like to download the gene expression data with GEO accession number "GSE104075" from GEO repository. here is my code: gset <- getGEO("GSE104075",GSEMatrix =TRUE, getGPL=TRUE, AnnotGPL=TRUE) if (length(gset) > 1) idx <- grep("GPL21298", attr(gset, "names")) else idx ...
atacseq geo getgeo rna-seq getquery written 7 months ago by bioyas0 • updated 7 months ago by ATpoint29k

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