Dear Sindrle,
Sorry for the crash of R -- did it crash within a function of Rsubread or somewhere else? The ".featureCount" files are indeed very big -- they contain the assignment result of each single read (or fragment) in the input SAM or BAM files, and is uncompressed. That is why they are usually larger than the input BAM files.
The format of the GTF file seemed perfectly correct. I tried to put the first couple of lines you provided into a GTF file, and ran featureCounts on a paired-end BAM file. The result seemed correct -- featureCounts loaded 3 features and 2 meta-features from the GTF file, and assigned 286 reads to the 2 meta-features. The R object returned from featureCounts has the correct numbers on each meta-feature.
The only problem is that your command line has an additional parameter "GTF.featureType=featureGENE". What was the value of variable featureGENE? The value should be "exon" for the GTF file you're using.
Cheers,
Yang
Sorry for the crash of R -- did it crash within a function of Rsubread or somewhere else? The ".featureCount" files are indeed very big -- they contain the assignment result of each single read (or fragment) in the input SAM or BAM files, and is uncompressed. That is why they are usually larger than the input BAM files.
The format of the GTF file seemed perfectly correct. I tried to put the first couple of lines you provided into a GTF file, and ran featureCounts on a paired-end BAM file. The result seemed correct -- featureCounts loaded 3 features and 2 meta-features from the GTF file, and assigned 286 reads to the 2 meta-features. The R object returned from featureCounts has the correct numbers on each meta-feature.
The only problem is that your command line has an additional parameter "GTF.featureType=featureGENE". What was the value of variable featureGENE? The value should be "exon" for the GTF file you're using.
Cheers,
Yang
Code:
========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 1.12.6 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || o A.bam || || || || Output file : ./.Rsubread_featureCounts_pid24234 || || Annotations : in.gtf (GTF) || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : no || || Strand specific : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || || \\===================== [url]http://subread.sourceforge.net/[/url] ======================// //================================= Running ==================================\\ || || || Load annotation file in.gtf ... || || Number of features is 3 || || Number of meta-features is 2 || || Number of chromosomes is 1 || || || || Process BAM file A.bam... || || Assign reads to features... || || Total number of reads is : 1124980 || || Number of successfully assigned reads is : 286 (0.0%) || || Running time : 0.05 minutes || || || || Read assignment finished. || || || \\===================== [url]http://subread.sourceforge.net/[/url] ======================//
Originally posted by sindrle
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