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Old 11-07-2012, 08:39 AM   #2
EGrassi
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Location: Turin, Italy

Join Date: Oct 2010
Posts: 66
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With tophat 2.0.4 the logs are similar but:
Code:
$ samtools flagstat accepted_hits.bam 
10819957 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
10819957 + 0 mapped (100.00%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
I'm beginning to think that maybe I should try STAR. Or that I definitely need 3 months to perform "unit tests" also on these well known, widely used and presented in literature tools.
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