Question: genomicFeature---paired end read::reads from the same pair were found not adjacent to each
0
gravatar for memoly101
9 months ago by
memoly1010
memoly1010 wrote:

Hi ,

For the following :

> fCountsList = featureCounts(props, annot.ext="/patho/to/gtf/GRCh38.gtf", isGTFA
nnotationFile=TRUE, nthreads=16, isPairedEnd=TRUE, allowMultiOverlap=TRUE, fraction=FALSE)

my job is killed by the following :

WARNING: reads from the same pair were found not adjacent to each  other in the input (due to read sorting by location or reporting of multi-mapping read pairs).                                                                                                   
    Pairing up the read pairs.

Any pieces of advice?

Thanks, Memol

normalization • 189 views
ADD COMMENTlink written 9 months ago by memoly1010

Is your job really killed? That is just a warning, rather than an error, and the manual for Rsubread suggests that this is the expected behaviour (see Section 3 of http://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/Rsubread.pdf)

ADD REPLYlink written 9 months ago by Mike Smith4.0k

Yeah, that's why I was surprised! I reinstalled the package and it worked. Thanks, Memol

ADD REPLYlink written 9 months ago by memoly1010
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