osvaldogc
commented
4 years ago Hello,
As for the case study analysis, we provided the genomic coordinates for those genes in BED format.
You can get a full gene annotation for GRCh37/hg19 from Gencode: https://www.gencodegenes.org/human/release_33lift37.html
Keep in mind that you must convert the GTF file with the gene annotation to BED format, in order for bicycle to be able to use it.
osvaldo.
From: freedomq8 [notifications@github.com] Sent: Wednesday, April 22, 2020 11:03 AM To: sing-group/bicycle Cc: Subscribed Subject: [sing-group/bicycle] Annotation and bed file for hg19 (#4)
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Hi there,
I wanted to ask a question regarding differential DMR analysis is there a way to get the annotation for hg19. I do have the Illumina manifest files one bed file with this structure: chr1 17363 17575 chr1_17364-17575 chr1 91548 91553 chr1_91549-91553 And another txt file with this structure: Chr Start Stop UCSC_CpG_Islands_Name Relation_to_UCSC_CpG_Island chr1 17363 17575 chr1 91548 91553 chr1 91570 91587 chr1 129279 129380 chr1 135141 135255 chr1:135124-135563 Island based on the case study demo analysis, I see some gene names. could you direct me how to get annotation file (hg19) to include for the analysis ?
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freedomq8
Hi there,
I wanted to ask a question regarding differential DMR analysis is there a way to get the annotation for hg19. I do have the Illumina manifest files one bed file with this structure: chr1 17363 17575 chr1_17364-17575 chr1 91548 91553 chr1_91549-91553 And another txt file with this structure: Chr Start Stop UCSC_CpG_Islands_Name Relation_to_UCSC_CpG_Island chr1 17363 17575 chr1 91548 91553 chr1 91570 91587 chr1 129279 129380 chr1 135141 135255 chr1:135124-135563 Island based on the case study demo analysis, I see some gene names. could you direct me how to get annotation file (hg19) to include for the analysis ?