User: g.sathish.k

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Posts by g.sathish.k

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Comment: C: extracting a specific field from .bed file and sort into new file
... Thank you very much! ...
written 25 days ago by g.sathish.k0
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Comment: C: extracting a specific field from .bed file and sort into new file
... Thank you very much ...
written 25 days ago by g.sathish.k0
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Comment: C: extracting a specific field from .bed file and sort into new file
... Thank you so much, it worked! :) ...
written 25 days ago by g.sathish.k0
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Comment: C: extracting a specific field from .bed file and sort into new file
... the new file should contain list of all gene names (from gene_name field), nothing else. Sorry, I just realized while copy pasting it cut off some fields. Here is the complete details for one gene from which i need just the gene name chr12 85065376 85065805 ENSG00000257296.1 . + HAVANA gene . ID=E ...
written 25 days ago by g.sathish.k0
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extracting a specific field from .bed file and sort into new file
... I have a test.bed file that contains the following: chr12 85430091 85657002 ENSG00000133640.14 . + HAVANA gene . ID=ENSG00000133640.14;gene_id=ENSG00000133640.14;transcript_id=ENSG00000133640.14;gene_type=protein_coding;gene_status=KNOWN;gene_name=LRRIQ1;transcript_type=protein_coding;transcrip ...
bed bash script shell python written 25 days ago by g.sathish.k0 • updated 25 days ago by Pierre Lindenbaum100k
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Comment: C: Genes around open regions
... Thanks Alex that really helped :) ...
written 9 weeks ago by g.sathish.k0
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Comment: C: Genes around open regions
... I want to use the release_19 of gencode so i made changes to the above code and was able to successfully generate genes.bed file. But, I couldn't get the "bedmap --echo --echo-map-id-uniq --range 25000 open-regions.bed genes.bed > answer.25kb.bed" code to work. It creates the output file but the ...
written 9 weeks ago by g.sathish.k0
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Comment: C: Genes around open regions
... Thank you Alex, I really appreciate your help. ...
written 9 weeks ago by g.sathish.k0
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Comment: C: Genes around open regions
... Thanks Jared, I appreciate it. ...
written 9 weeks ago by g.sathish.k0
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Genes around open regions
... Hello Everyone! I am new here and new to field of genomics and informatics. Recently we generated ATAC-seq data of normal and cancer cells.. The data shows open regions in cancer cells compared to normal cells. I would like to know if there is a program out there to generate a list of genes that a ...
gene genes open atac-seq written 9 weeks ago by g.sathish.k0 • updated 9 weeks ago by Alex Reynolds21k

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