User: arsala521

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arsala52110
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Posts by arsala521

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Comment: C: Getting human-specific regions of the human genome
... Thank you for the guide. I will look into more details. ...
written 7 weeks ago by arsala52110
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Comment: C: Getting human-specific regions of the human genome
... Okay, thank you for the guide. I will look into these details. ...
written 7 weeks ago by arsala52110
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Comment: C: Getting human-specific regions of the human genome
... Thank you. Just looked into this paper. What I understood is, it is about identifying unique regions within a single genome. ...
written 7 weeks ago by arsala52110
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Comment: C: Getting human-specific regions of the human genome
... Thank you, but I have more intergenic regions in my starting list. ...
written 7 weeks ago by arsala52110
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Getting human-specific regions of the human genome
... Hi everyone, I have a list of human genomic regions (bed file enlisting genomic coordinates). From that list I want to extract those regions which are human-specific. I want to ask what can be appropriate pipeline for that. I found one study using this pipeline: Using liftOver utility for converti ...
human-specific regions written 7 weeks ago by arsala52110 • updated 7 weeks ago by Alex Reynolds31k
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Comment: C: TSS of canonical transcripts
... Thank you. I could work in that way. The APPRIS file is for GENCODE 34 dataset and the GTF file from GENCODE is for release 35. Would it be okay to match transcript ids between these two files? ...
written 5 months ago by arsala52110
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Comment: C: TSS of canonical transcripts
... Thank you. APPRIS does provide the required information but I am not sure how to extract it. The APPRIS file for GENCODE 34 dataset is like this: SCYL3 ENSG00000000457 ENST00000367772 CCDS1287.1 PRINCIPAL:4 SCYL3 ENSG00000000457 ENST00000367771 CCDS1286.1 ALTERNATIVE:2 SCYL3 ENSG000000 ...
written 5 months ago by arsala52110
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Comment: C: TSS of canonical transcripts
... Thank you. It really helped but I think it doesn't cover all protein coding genes. By analyzing its GTF file, I found it has 16,230 genes in total. ...
written 5 months ago by arsala52110
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TSS of canonical transcripts
... Hi everyone, I need TSS (transcription start site) of all the protein coding genes in human genome. I only want to focus on canonical transcripts and want one TSS per gene. Can someone please tell me which file from which source can provide this information? I tried refGene.txt file from UCSC, an ...
canonical transcripts tss written 5 months ago by arsala52110 • updated 5 months ago by ATpoint46k
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Comment: C: TSS of protein coding genes
... Thank you. It really helped. ...
written 6 months ago by arsala52110

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