MEDIPS test data lack of 4 files
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@yanzhangusa-8465
Last seen 6.3 years ago

Accroding to Mannual, there should be 8 files for testing datasets: hESCs.MeDIP.Rep1.chr22.bam (7.6M), hESCs.MeDIP.Rep2.chr22.bam(14M), hESCs.MeDIP.Rep3.chr22.bam (9.1M), hESCs.Input.chr22.bam
(4.9M), DE.MeDIP.Rep1.chr22.bam (12M), DE.MeDIP.Rep2.chr22.bam (14M),DE.MeDIP.Rep3.chr22.bam (13M), and DE.Input.chr22.bam (11M).

But when I install medipsdata, there are only 4 files: hESCs.MeDIP.Rep1.chr22.bam (7.6M), hESCs.MeDIP.Rep2.chr22.bam(14M), hESCs.Input.chr22.bam(4.9M), and  DE.Input.chr22.bam (11M)

 

Could you add the rest of 4 files? or where I could download those 4 files?

 

Thanks

yan

medips • 621 views
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Lukas Chavez ▴ 570
@lukas-chavez-5781
Last seen 3.7 years ago
USA/La Jolla/UCSD
Dear Yan, indeed, the MEDIPSData package has been generated based on sequencing data from 8 samples (3x MeDIP hESCs, 3x MeDIP differentiated hESCs, 1x Input hESCs, 1x Input differentiated hESCs; data is provided for chromosome 22 only). However, bam files are included in the MEDIPSData package for only four samples (2x MeDIP hESCs, 1x Input hESCs, and 1x Input differentiated hESCs; chr22 only) which are located in the inst/extdata subfolder of the MEDIPSData package. The remaining bam files have been preprocessed and are stored as RData objects in the data subfolder of the MEDIPSData package. Detailed information on how the bam files have been preprocessed can be found by loading the MEDIPSData library followed by e.g. > ?hESCs_MeDIP Please bare with me that I do not have the remaining chr22 example bam files available anymore. All the sequencing data of this study has been submitted to NCBI Sequence Read Archive under accession no. SRA012665. All the best, Lukas On 23 Jul 2015, at 23:44, yanzhangusa [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User yanzhangusa<https: support.bioconductor.org="" u="" 8465=""/> wrote Question: MEDIPS test data lack of 4 files<https: support.bioconductor.org="" p="" 70321=""/>: Accroding to Mannual, there should be 8 files for testing datasets: hESCs.MeDIP.Rep1.chr22.bam (7.6M), hESCs.MeDIP.Rep2.chr22.bam(14M), hESCs.MeDIP.Rep3.chr22.bam (9.1M), hESCs.Input.chr22.bam (4.9M), DE.MeDIP.Rep1.chr22.bam (12M), DE.MeDIP.Rep2.chr22.bam (14M),DE.MeDIP.Rep3.chr22.bam (13M), and DE.Input.chr22.bam (11M). But when I install medipsdata, there are only 4 files: hESCs.MeDIP.Rep1.chr22.bam (7.6M), hESCs.MeDIP.Rep2.chr22.bam(14M), hESCs.Input.chr22.bam(4.9M), and DE.Input.chr22.bam (11M) Could you add the rest of 4 files? or where I could download those 4 files? Thanks yan ________________________________ Post tags: medips You may reply via email or visit MEDIPS test data lack of 4 files Dr. Lukas Chavez Division of Pediatric Neurooncology Group Leader Computational Oncoepigenomics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 280 69120 Heidelberg Germany phone: +49 6221 42-4676 mobile: +49 172 158 8231 l.chavez@dkfz.de<mailto:l.chavez@dkfz.de> www.dkfz.de<http: www.dkfz.de=""><http: www.dkfz.de=""/> https://www.dkfz.de/en/paediatrische-neuroonkologie/index.php http://pediatric-neurooncology.dkfz.de/index.php/en/research/pediatric-neurooncology/bioinformatics [cid:A23DCB56-6826-4A7D-AB02-51FE00A96626@dkfz-heidelberg.de] Management Board: Prof. Dr. Dr. h.c. Otmar D. Wiestler, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Confidentiality Note: This message is intended only for the use of the named recipient(s) and may obtain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited.
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