User: arsala521
arsala521 • 10
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Posts by arsala521
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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 10 weeks ago by
arsala521 • 10
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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 10 weeks ago by
arsala521 • 10
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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 10 weeks ago by
arsala521 • 10
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... 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 ...
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C: TSS of protein coding genes
... Thank you. It really helped. ...
written 3 months ago by
arsala521 • 10
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... Hi everyone,
I want to have transcription start sites (TSS) of all protein-coding genes in the genome. There is a couple of things I want to ask about.
I found two relevant files for gene coordinates at UCSC browser: refGene.txt.gz (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.t ...
written 3 months ago by
arsala521 • 10
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3
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Comment:
C: Bigwig To Wig Conversion
... Can you please share the link from where you installed bigWigToWig? Thank you ...
written 3 months ago by
arsala521 • 10
0
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1
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151
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1
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... Hello everyone,
Is there any option in bedtools or bedops that after merging show the original regions of the merged interval as well?
For example for the following input
chr1 500 1000
chr1 750 1000
chr2 200 500
can I have the output somewhat like this
chr1 500 1000 chr1 500 100 ...
written 8 months ago by
arsala521 • 10
• updated
8 months ago by
Kevin Blighe ♦ 67k
0
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525
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... Thank you so much for helping me out ...
written 9 months ago by
arsala521 • 10
0
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1
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525
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1
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... Thank you
Do you know if we can do this in shell with awk command? ...
written 9 months ago by
arsala521 • 10
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