process-chipseq.R Error in rbindlist(bplapply(files, guessFqEncodingByFile))

[crazyhottommy]

I was running pRSEM https://github.com/deweylab/RSEM/issues/54 , everything was fine until this step:

Error in rbindlist(bplapply(files, guessFqEncodingByFile)) :
  attempt to set an attribute on NULL
Calls: main -> <Anonymous> -> rbindlist

I grep and saw this code is from the process-Chipseq.R, any guess what is possibly wrong here? Thanks, Tommy

[pliu55]

@crazyhottommy

Did you experience the same issue when running pRSEM's demo?

This code is using the ShortRead library to guess your ChIP-seq FASTQ's encoding, e.g. phred33, phred64, etc. We utilize the BiocParallel to parallel this process. Could you try the bplapply function on your system and see if there's any issue with it?

[crazyhottommy]

I installed it and bplapply works, but still same error. I decide to use the peak mode to get away processing the raw ChIP-seq data, so for the -chipseq-target-peak-file the input is in narrowpeak format, if I only have peaks with 3 columns, chr, start, end. can I use it? does p-RSEM use other columns (e.g. score, pvalues) ?

Thanks!

[pliu55]

@crazyhottommy

pRSEM only uses chr, start, and end, and does not use info from the other columns, but pRSEM assumes the input peak file is in gzipped and have 10 columns (as following the narrowpeak format). So please:

• add 7 columns of NA (or whatever info you prefer) to your peak file
• gzip it

Just for the reference, line 513-516 in process-rnaseq.R should be the code that reads peak file and I paste them below:

    data.table(read.table(gzfile(fchipseq_peaks), header=F, sep="\t",
                          colClasses=c('character', 'numeric',
                                       'numeric', rep('NULL', 7))))

I am going to close this issue. If you encountered any problem in using pRSEM's -chipseq-target-peak-file, please open a new one. Thanks for using pRSEM.

[crazyhottommy]

thanks! this is helpful.