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Question: problem running featurecounts using hg38 in-built annotation
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gravatar for raf4
5 months ago by
raf420
raf420 wrote:

Dear List,

I am having trouble running feature counts as implemented in Rsubread on my mac

My script is:

library(Rsubread)

b1.res<-featureCounts(files="b1.res.bam",annot.inbuilt="hg38",isPairedEnd=TRUE,requireBothEndsMapped=FALSE)

I get an output file with numbers instead of gene names and no counts.

I have 2 warning messages.

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).                        ||
||                                                                            ||
||    Read re-ordering is performed.           

and

warning message:
package ‘Rsubread’ was built under R version 3.3.3

(I am using 3.3.2)

I am not reproducing the whole output file because I get a

"language "af" is not one of the supported languages ['en']!"

from the site.

Thanks and best wishes,

Rich

Richard Friedman

 

 

 

ADD COMMENTlink written 5 months ago by raf420

I believe I found the problem. I should  not have used the patched sequence.

I am currently downloading


ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/ GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

If this is not the right version of the sequence, please let me know.

Thanks and best wishes,

Rich

 

 

ADD REPLYlink written 5 months ago by raf420

Hi Rich, could you please provide the complete output from your featureCounts run? Also you should update your copy of Rsubread and Bioc to their latest version as well.

ADD REPLYlink written 5 months ago by Wei Shi2.7k
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