User: BioProg

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BioProg0
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Posts by BioProg

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Comment: C: How to identify which genes fall within genomic locations
... i double check.d. my bad, the result is just a representation of multiple overlaps. I thought it just matches one to one. Thanks.    ...
written 3.3 years ago by BioProg0
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Comment: C: How to identify which genes fall within genomic locations
... Here is what I did: I downloaded a reference file from UCSC hg19 and fixed columns to have this structure: chr1 11868 14409 ENST00000456328 ENSG00000223972 + 3 chr1 11871 14412 ENST00000515242 ENSG00000223972 + 3 chr1 11873 14409 ...
written 3.3 years ago by BioProg0
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Comment: C: How to identify which genes fall within genomic locations
... Hi Alex- I am not an expert in this. I was able to download file by going to the link below (i dont have wget function) ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_21/gencode.v21.annotation.gff3.gz, i unzipped it, I then installed BEDOPS and tried: gff2bed --input=unzipd.gencode.v21. ...
written 3.3 years ago by BioProg0
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Comment: C: How to identify which genes fall within genomic locations
... Hi Alex- I am not an expert in this. I was able to download file by going to the link below (i dont have wget function) ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_21/gencode.v21.annotation.gff3.gz, i unzipped it, I then installed BEDOPS and tried: gff2bed --input=unzipd.gencode.v21. ...
written 3.3 years ago by BioProg0
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Comment: C: How to identify which genes fall within genomic locations
... oh nice, but what would my reference to intersect to be? That's the problem I cant find a file with "GeneID" "GeneName" Chromosome location.   ...
written 3.3 years ago by BioProg0
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How to identify which genes fall within genomic locations
... I have an extended list of gene locations (chr#, start and end site) with respect to hg19 as extracted from not very specific alignments. I would like to find which genes fall in each of the regions (which consists of >20,000). For instance: chr1:33183334-33190838 chr10:93066718-93371217 I woul ...
genomic location hg19 written 3.3 years ago by BioProg0 • updated 3.3 years ago by Alex Reynolds28k
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Comment: C: chromosome name in summarizeOverlaps for RNASeq data
... You are right I should have used readRDS as i saved file as RDS. Thank you ...
written 3.4 years ago by BioProg0
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Answer: A: how to add a pseduo gene into a GTF file?
... Do you mean that your GTF file contains the pseudogene annotations but the cufflinks output does not have the "biotype/function" of the transcript and gene IDs? if so, i can share with you a script to extract that.  ih ad the same problem last week. ...
written 3.4 years ago by BioProg0
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chromosome name in summarizeOverlaps for RNASeq data
...  For a while I used quantile normalization followed by t-test or cuffdiff for analysis of RNASeq. I would like to try DESeq2 given its better normalization method based on the readings. I am using your R package summarizeOverlaps to create count tables as I found it to be the easiest. However, I am ...
annotation deseq2 summarizeoverlaps rna-seq written 3.4 years ago by BioProg0 • updated 3.4 years ago by Devon Ryan90k

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