Entering edit mode
mmurshed
•
0
@mmurshed-15066
Last seen 6.2 years ago
i just created 16 BAM file by using Rsubread packege. When i run the featurecounts then I only get the total counts for each of the BAM file but not getting the count matrix.
when i use fc$counts it shows
DAB1.BAM DAB2.BAM ......... DAB16.BAM
15969703 1760659 ...............1505869
but i am not getting any count matrix for each gene.
can anyone help me with this.
Thanks,
Monzur Murshed
You need to show the code you used.
i am using this codes:
library(Rsubread)
> a<-list.files(pattern="*.BAM")
> a
[1] "DAB1.BAM" "DAB10.BAM" "DAB11.BAM" "DAB12.BAM" "DAB13.BAM" "DAB14.BAM"
[7] "DAB15.BAM" "DAB16.BAM" "DAB2.BAM" "DAB3.BAM" "DAB4.BAM" "DAB5.BAM"
[13] "DAB6.BAM" "DAB7.BAM" "DAB8.BAM" "DAB9.BAM"
fc<-featureCounts(a,annot.ext="C_albicans_subset.gff",isGTFAnnotationFile=TRUE,GTF.featureType="exon",GTF.attrType="gene_id")
when i run this code it shows some warning
Warning: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
The specified gene identifier attribute is 'gene_id'
The attributes included in your GTF annotation are 'ID=C1_00010W_A-T-E1;Parent=C1_00010W_A-T'
|| Features : 13831 ||
|| Meta-features : 1 ||
|| Chromosomes/contigs : 17
when i use this command i get only this out put not any count matrix
> fc$counts DAB1.BAM DAB10.BAM DAB11.BAM DAB12.BAM DAB13.BAM DAB14.BAM DAB15.BAM <NA> 15969707 16514867 16255504 15581557 15506982 16257617 16074052 DAB16.BAM DAB2.BAM DAB3.BAM DAB4.BAM DAB5.BAM DAB6.BAM DAB7.BAM DAB8.BAM <NA> 15867891 16261658 12829747 16252618 15411383 14922696 15855204 16096131 DAB9.BAM <NA> 18413643 >