<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Fabien,<div class="">We don’t have a simple list of the samples that we used. But you can retrieve this information from the FTP.</div><div class=""><br class=""></div><div class="">To get the list of the names of the samples, you can either look in the README which will have the list or you can look at the name of the BAM files, they are in the format <assembly name>.<provider>.<sample name>.<version>.bam</div><div class=""><br class=""></div><div class="">From the BAM files you can retrieve the sample accession(s) for the “sample”. When there is multiple accession for the same tissue name, we merge the data.</div><div class=""><br class=""></div><div class="">For the current annotation on GRCg7b, these files are not yet available on the FTP and you will need to wait for release 108. However we use the same set that was used for the latest GRCg6a annotation with the addition of the data from the GENE-SWitCH project.</div><div class=""><br class=""></div><div class="">Thanks</div><div class="">Thibaut<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 12 Aug 2022, at 18:47, Fabien Degalez <<a href="mailto:fabien.degalez@inrae.fr" class="">fabien.degalez@inrae.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class="">Hi everyone,<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class="">I would like to know if it's possible to have access to the list of RNA-seq samples used for the gene annotation (more precisely for the chicken one, even if i think that is the same for all the others).<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class="">Indeed, on the PDF linked to gene annotation, it just says that "samples from ENA were used" but without any more precision.<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class="">I don't know if I should use the API or if the information is on the website or on the FTP server.<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class="">Thank you for your help.<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class="">Bests<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class="">Fabien DEGALEZ<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><br class=""></div><div id="Signature" style="caret-color: rgb(0, 0, 0); font-family: Verdana, Geneva, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; 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