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featureCounts also outputs assignment stat in a .summary file. Could you show the content of that file?
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Obvious thing to check - if chromosome names in your sam file match the annotation.
There are 270 "chromosomes" since there are entries of things like (besides the standard chromosomes 1,2,3 etc)
CHR_HSCHR9_1_CTG2
CHR_HSCHR17_5_CTG4
CHR_HSCHR16_4_CTG1
CHR_HSCHR19_5_CTG2
CHR_HSCHR9_1_CTG4
CHR_HSCHR19_4_CTG2
KI270726.1
KI270711.1
KI270714.1
KI270713.1
CHR_HSCHR12_5_CTG2)
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featureCounts: 270 chr in GRCh38 and only assigning 1.5%?
INPUT
Stranded RNAseq, 101bp Illumina paired end reads mapped to GRCh38 release 78 using star.
COMMAND
featureCounts -a Homo_sapiens.GRCh38.78.gtf -o mySAMPLE/mySAMPLE.featureCounts -F GTF -t exon -g gene_name -s 1 -T 10 -p -P mySAMPLE/Aligned.out.sam
QUESTIONS
1. Why does it say, that 'ftp://ftp.ensembl.org/pub/release-78/gtf/homo_sapiens/Homo_sapiens.GRCh38.78.gtf.gz' has 270 chromosomes?
2. What could be the reason for the low fragment assignment, 697168 / 46248243 = 1.5%
3. Have I used wrong options?
Cheers!Tags: None
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