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@tomsing1
Created February 1, 2016 16:20
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Example of a qualimap RNAseq report for paired-end data
RNA-Seq QC report
-----------------------------------
>>>>>>> Input
bam file = /tmp/07122375.bam
gff file = /mnt/annotation.gtf
counting algorithm = uniquely-mapped-reads
protocol = strand-specific-forward
>>>>>>> Reads alignment
reads aligned (left/right) = 3,295,794 / 3,295,797
read pairs aligned = 3,295,792
total alignments = 7,758,876
secondary alignments = 1,167,285
non-unique alignments = 1,511,158
aligned to genes = 1,329,862
ambiguous alignments = 28,642
no feature assigned = 1,650,052
not aligned = 2,596,101
>>>>>>> Reads genomic origin
exonic = 1,329,862 (44.63%)
intronic = 1,032,186 (34.64%)
intergenic = 617,866 (20.73%)
overlapping exon = 156,843 (5.26%)
>>>>>>> Transcript coverage profile
5' bias = 0.82
3' bias = 0.67
5'-3' bias = 1.18
>>>>>>> Junction analysis
reads at junctions = 1,434,012
ACCT : 4.86%
AGGT : 4.8%
AGGA : 3.61%
TCCT : 3.49%
ATCT : 3.2%
AGCT : 3.09%
AGGC : 2.55%
GCCT : 2.51%
CCCT : 2.46%
AGAT : 2.38%
AGGG : 2.19%
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