Question: chromosome name in summarizeOverlaps for RNASeq data
gravatar for BioProg
3.2 years ago by
BioProg0 wrote:

 For a while I used quantile normalization followed by t-test or cuffdiff for analysis of RNASeq. I would like to try DESeq2 given its better normalization method based on the readings. I am using your R package summarizeOverlaps to create count tables as I found it to be the easiest. However, I am encountering couple of issues. First,the ensemble-based gtf file that I used to align all my mouse RNAseq data has the chromosomes named as “1, 2 , 3”… Rather than “chr1 , chr2 ..”. My Testing R code for summarizeOverlaps is as follows:




saveDb(TxDb_mm10, file="mm10.sqlite”)


exbyGene<-exonsBy(mm10,by="gene”) #I assume this is assigning things by GENES ids (ENSG..)

exbyTx<-exonsBy(mm10,by="tx”) #I assume this is assigning things by Transcript IDS (ENST…)


fls <- list.files(“Path/To/BamFiles", pattern=".accepted_hits.bam", full= TRUE)

grp1<- fls[1]

grp2 <- fls[c(2,3)]



head(seqlevels(TxDb_mm10)) # this shows that the mm10 sqlite I am using has chr1, chr2 .. Format

seqinfo(bamLst_grp1) #this shows that the chromosome names for my testing bam files are 1, 2, 3…



##Saving environment

saveRDS(se_grp1, file="se_grp1.Rdata")

saveRDS(se_grp2, file="se_grp2.Rdata”)


While the script runs nicely (and please, advice me if I should optimize anything as I have basic understanding of each of the commands), when I tried to load the environment I am getting the following error:


Error: bad restore file magic number (file may be corrupted) -- no data loaded

In addition: Warning message:

file ‘se_grp2.Rdata’ has magic number 'X'

  Use of save versions prior to 2 is deprecated 


Also, I am not sure if the error is because the chromosome names are incompatible between the reference and bam file. If that’s the case, how can I correct for this? 

ADD COMMENTlink modified 3.2 years ago by Devon Ryan88k • written 3.2 years ago by BioProg0
gravatar for Devon Ryan
3.2 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

The error is unrelated to any chromosome names and has to do with R not being able to load the file it saved. Presumably there was a (hopefully transient) storage problem.

ADD COMMENTlink written 3.2 years ago by Devon Ryan88k

You are right I should have used readRDS as i saved file as RDS.

Thank you

ADD REPLYlink written 3.2 years ago by BioProg0
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