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.
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,
On 23 Jul 2015, at 23:44, yanzhangusa [bioc] <firstname.lastname@example.org<mailto:email@example.com>> wrote:
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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?
Post tags: medips
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Dr. Lukas Chavez
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German Cancer Research Center (DKFZ)
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