FeatureCounts

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Setshaba Taukobong

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Apr 14, 2020, 8:55:10 AM4/14/20

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Hi All,

I am trying to generate count matrices using the following code:

E.coli_sample <-featureCounts(files="/home/setshaba/Desktop/Masters/P25_1.bam",annot.ext="/home/setshaba/Desktop/Masters/E.coli_Data/Reference/E.coli_BAA196_NC.joint.v0.gff",GTF.attrType="locus_tag",isGTFAnnotationFile=TRUE,GTF.featureType="CDS",useMetaFeatures=TRUE)

I am however getting the warning below. I believe that the names from the BAM file do not match to those from the GFF file. I however do not know how to correct this.

I have attached the BAM file and GFF file (https://drive.google.com/file/d/1XGxAmMFJNdmsQYb5LPibHWFj2c2Wm6xH/view?usp=sharing)

Could I please get some assistance on this. Thank you, Setshaba

Rsubread 1.28.1

//========================== featureCounts setting ===========================\\

|| ||

|| Input files : 1 BAM file ||

|| S /home/setshaba/Desktop/Masters/P25_1.bam ||

|| ||

|| Dir for temp files : . ||

|| Threads : 1 ||

|| Level : meta-feature level ||

|| Paired-end : no ||

|| Strand specific : no ||

|| Multimapping reads : not counted ||

|| Multi-overlapping reads : not counted ||

|| Min overlapping bases : 1 ||

|| ||

\\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\\

|| ||

|| Load annotation file /home/setshaba/Desktop/Masters/E.coli_Data/Refere ... ||

Warning: failed to find the gene identifier attribute in the 9th column of the provided GTF file.

The specified gene identifier attribute is 'Locus_tag'

The attributes included in your GTF annotation are 'name=CDS;db_xref=SEED:fig|562.40054.peg.1233;translation=MSLSLWQQCLARLQDELPATEFSMWIRPLQAELSDNTLALYAPNRFVLDWVRDKYLNNINGLLTSFCGADAPQLRFEVGTKPVTQTPQAAVTSNVAAPAQVAQTQPQRAAPSTRSGWDNVPAPAEPTYRSNVNVKHTFDNFVEGKSNQLARAAARQVADNPGGAYNPLFLYGGTGLGKTHLLHAVGNGIMARKPNAKVVYMHSERFVQDMVKALQNNAIEEFKRYYRSVDALLIDDIQFFANKERSQEEFFHTFNALLEGNQQIILTSDRYPKEINGVEDRLKSRFGWGLTVAIEPPELETRVAILMKKADENDIRLPGEVAFFIAKRLRSNVRELEGALNRVIANANFTGRAITIDFVREALRDLLALQEKLVTIDNIQKTVAEYYKIKVADLLSKRRSRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLREESHDIKEDFSNLIRTLSS;locus_tag=ECNC_0001;product=Chromosomal replication initiator protein DnaA;transl_table=11'

|| Features : 4960 ||

|| Meta-features : 1 ||

|| Chromosomes/contigs : 1 ||

|| ||

|| Process BAM file /home/setshaba/Desktop/Masters/P25_1.bam... ||

|| Single-end reads are included. ||

|| Assign reads to features... ||

|| Total reads : 140504 ||

|| Successfully assigned reads : 0 (0.0%) ||

|| Running time : 0.02 minutes ||

|| ||

|| Read assignment finished. ||

|| ||

\\===================== http://subread.sourceforge.net/ ======================//

E.coli_BAA196_NC.joint.v0.gff

P25_1.bam.indel

Yang LIAO

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Apr 15, 2020, 7:05:48 AM4/15/20

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Your annotation file contains many long lines. There was a bug making Rsubread unable to parse the annotation when the lines are too long, but it has been fixed. You may upgrade to the latest version of Rsubread: