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Tophat singleton behaviour & Flagstats output
Dear all,
I have a paired end (2x75) Illumina data and I aligned these reads with TopHat v1.2.0.
I performed a samtools flgstat analysis of my files.bam and an output example is:
5033547 in total
0 QC failure
0 duplicates
5033547 mapped (100.00%)
5033547 paired in sequencing
3665556 read1
1367991 read2
794 properly paired (0.02%)
638862 with itself and mate mapped
4394685 singletons (87.31%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
I have too much singletons and a lower numbers of properly paired reads..
How Tophat mapps these singletons reads?
How Tophat acts towards of these unpaired reads? Does Tophat align these reads separately?
I don't know if these reads are very instructive or if I mistake something in TopHat command but I performed the same analysis with other trial data and I obtained 60-70% of properly paired reads.....
I have a paired end (2x75) Illumina data and I aligned these reads with TopHat v1.2.0.
I performed a samtools flgstat analysis of my files.bam and an output example is:
5033547 in total
0 QC failure
0 duplicates
5033547 mapped (100.00%)
5033547 paired in sequencing
3665556 read1
1367991 read2
794 properly paired (0.02%)
638862 with itself and mate mapped
4394685 singletons (87.31%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)
I have too much singletons and a lower numbers of properly paired reads..
How Tophat mapps these singletons reads?
How Tophat acts towards of these unpaired reads? Does Tophat align these reads separately?
I don't know if these reads are very instructive or if I mistake something in TopHat command but I performed the same analysis with other trial data and I obtained 60-70% of properly paired reads.....
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