genomicFeature---paired end read::reads from the same pair were found not adjacent to each

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memoly101 • 0

@memoly101-19491

Last seen 5.8 years ago

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 • 852 views

ADD COMMENT • link updated 5.8 years ago by Martin Morgan 25k • written 5.8 years ago by memoly101 • 0

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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 REPLY • link 5.8 years ago Mike Smith ★ 6.6k

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

ADD REPLY • link 5.7 years ago memoly101 • 0

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