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February 1, 2016 16:20
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Example of a qualimap RNAseq report for paired-end data
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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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