Question: How to enter mapped bam file in MEDIPS.R bioconductor package?
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gravatar for rousselene.jones
5 months ago by
rousselene.jones0 wrote:

Hi!

I am using MEDIPS.R package to analyze 45 methylated files. I have 45 files before pull down that i consider to be my Input_files for each 45 files after pull down considered to be my methylated files. I am running into issues when it come to create the MEDIPSData sets with them. I have 4 groups for which I create a vector containing replicates of each set:

Example;
bamfileHN=c("18mS5S10R1001trimmed.fq.gz.bam", "19mS2R1001trimmed.fq.gz.bam", "20m-2S6R1001trimmed.fq.gz.bam", "21m-2S6R1001trimmed.fq.gz.bam", "22mS3R1001trimmed.fq.gz.bam") and

inputHN=c("18iS3S8R1001trimmed.fq.gz.bam", "19iS2R1001trimmed.fq.gz.bam", "20i-2S3R1001trimmed.fq.gz.bam", "21i-2S4S12R1001trimmed.fq.gz.bam", "22iS6R1001_trimmed.fq.gz.bam")

But when I call for

HC=lapply(X=bamfileHC,FUN=MEDIPS.createSet,BSgenome = BSgenome, extend = extend, shift = shift, uniq = uniq,windowsize = ws) HN=lapply(X=bamfileHN,FUN=MEDIPS.createSet,BSgenome = BSgenome, extend = extend, shift = shift, uniq = uniq,windowsize = ws)

ECinput=MEDIPS.createSet(file=inputEC,BSgenome = BSgenome, extend = extend, shift = shift, uniq = uniq,windowsize = ws) ENinput=MEDIPS.createSet(file=inputEN,BSgenome = BSgenome, extend = extend, shift = shift, uniq = uniq,windowsize = ws)

trying to create MEDIPsets to compare these two datasets, I am getting this message "Please note, no data in the alignment file for chromosome(s): chr1 chr1GL45621.... chrY chrYJH584300random chrYJH584301random chrYJH584302random chrYJH" it is showing no data for all 19 chromosomes...

My bam files are not empty, what could be causing this? Also it is not clear to me how MEDIP concatenate the different replicate in one group to create a set. Their test data is working really well, so I am guessing that i need some help on how to input my data properly. They how t concatenate two file to create a MEDIPset, but how about with 6-8 files? and I notice two input files instead of one, where would the other input file come from? thanks,

Roxy

software error • 73 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by rousselene.jones0
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