User: oussama.badad

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Posts by oussama.badad

<prev • 5 results • page 1 of 1 • next >
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Calculating short read coverage at genome wide windows for create.set- MEDIPS
... Hi all i am trying to create set for my medipseq data , here is my command                         AKM-ANF_MeDIP = MEDIPS.createSet(file = "/scratch/obadad/MEDIP-Seq_BAMs/AKM-ANF-mapped.sorted.bam", BSgenome = "BSgenome.Oeuropaea.IOGC.v1", extend = 300, shift = 0, uniq = 1e-3, window_size = 100) ...
createset medip-seq written 5 months ago by oussama.badad0 • updated 4 months ago by Bioconductor Community ♦♦ 0
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Comment: C: create.set on MEDIPS
... Hi Lukas yes indeed , first i installed the BSgenome R CMD INSTALL BSgenome.Oeuropaea.IOGC.v1_1.0.tar.gz * installing to library ‘/scratch/obadad/anaconda3/envs/medip/lib/R/library’ * installing *source* package ‘BSgenome.Oeuropaea.IOGC.v1’ ... ** R ** inst ** byte-compile and prepare package for ...
written 6 months ago by oussama.badad0
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create.set on MEDIPS
... Hi i am tying to import my bam files for MEDIP-seq analysis, using a custom BSgenome . my bam files are in "MEDIPS_BAMs" directory i am using the following command : > AKM-ANF_MeDIP = MEDIPS.createSet(file = "MEDIPS_BAMs/AKM-ANF.sorted.bam", BSgenome = BSgenome.Oeuropaea.IOGC.v1, extend = 300 ...
medips createset written 6 months ago by oussama.badad0 • updated 6 months ago by Lukas Chavez510
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error importing bam file for MEDIPS analysis
... Hi i am tying to import my bam files for MEDIP-seq analysis. my bam files are in "MEDIPS_BAMs" directory i am using the following command : > AKM-ANF_MeDIP = MEDIPS.createSet(file = "MEDIPS_BAMs/AKM-ANF.sorted.bam", BSgenome = BSgenome.Oeuropaea.IOGC.v1, extend = 300, shift = 0, uniq = TRUE, ...
medips bamfile written 6 months ago by oussama.badad0 • updated 4 months ago by Bioconductor Community ♦♦ 0
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BSgenome package building
... Hi all, i am trying to build a BSgenome package for olea europea for some Medipseq analysis , i run the first command library(BSgenome) > forgeBSgenomeDataPkg("path/to/my/seed") it working and creating the single_sequences.2bit the when i run the second command R CMD build /scratch/obadad/BS ...
bsgenome written 7 months ago by oussama.badad0 • updated 7 months ago by James W. MacDonald50k

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