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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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isSecondaryAlignment error #67

Open girdhar3 opened 7 years ago

girdhar3 commented 7 years ago

Hi I am trying to get tss map for a set of genes

here is my code

ngs.plot.r -G hg19 -R tss -C bamfile -O bamfile.tss -T H3K4me3 -L 3000 -E /genelist -F protein_coding

genelist format ENSG00000270986 ENSG00000077782 ENSG00000272048 ENSG00000015532 ENSG00000100902 ENSG00000165548

bam file is sorted

@HD VN:1.5 SO:coordinate @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431

@PG ID:bwa PN:bwa

ERROR

Loading R libraries.....Done Analyze bam files and calculate coverageWarning message: 'isNotPrimaryRead' is deprecated. Use 'isSecondaryAlignment' instead. See help("Deprecated") ...........................................Error in { : task 1 failed - "object 'isize' not found" Calls: covMatrix -> %dopar% -> Execution halted

Do you know why?

jdblischak commented 7 years ago

The warning message about the argument isNotPrimaryRead appears to have been fixed in the most recent commit: https://github.com/shenlab-sinai/ngsplot/commit/c8f1265309174fc7e440fa554948ed0faa6b1f32 What version are you using? Can you try downloading the latest version and re-run your command?

That's just a warning though, so I am doubtful if that will solve the error about not finding the object isize. My guess is that if you are subsetting with Ensembl gene IDs but your reads are mapped to the UCSC chromsomes, that the chromosome names are incompatible. What happens when you run your command omitting the -E option?

Also, did you run -E /genelist as you wrote or -E genelist?