Annotation and bed file for hg19

[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 ?

[osvaldogc]

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.

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________________________________ 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) CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe 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 ? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#4>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADDOQK3HA7ZWE2UJ26FLLQDRN2XGTANCNFSM4MN7JUKA>. **ADVERTENCIA LEGAL**: Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protección de los datos personales de las personas físicas, la información personal que nos pueda facilitar a través de este correo electrónico quedará registrada por la Fundación CNIO con la finalidad de tramitar el objeto del presente correo electrónico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no serán comunicados a ningún destinatario salvo a aquellos que usted nos autorice o así venga exigido por una ley. Ud. podrá ejercer los derechos de acceso, rectificación, supresión, limitación de tratamiento, portabilidad y oposición en la siguiente dirección: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con el Delegado de Protección de Datos en: delegado_lopd@cnio.es. Para el caso de que Ud. precise conocer información adicional sobre el tratamiento de sus datos personales, puede consultar dicha información adicional en el siguiente enlace dentro de nuestra página web: https://www.cnio.es/es/privacidad/index.asp **LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message. Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protección de Datos) at: delegado_lopd@cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp

[freedomq8]

Thanks, will give it a try.