Dear Alex,
I am currently using STAR on a new strand-specific paired-end RNA-seq dataset, and I am very happy with the output.
I just have one question though (as a matter of interest really), does STAR calculate the MAPQ value for the reads? I am asking because at the moment with my new dataset (and also with a simulated dataset) all my mapped reads have a MAPQ value of 255, see below:
Thanks a lot for you help, regards,
Nicolas
I am currently using STAR on a new strand-specific paired-end RNA-seq dataset, and I am very happy with the output.
I just have one question though (as a matter of interest really), does STAR calculate the MAPQ value for the reads? I am asking because at the moment with my new dataset (and also with a simulated dataset) all my mapped reads have a MAPQ value of 255, see below:
Code:
FCC1GLHACXX:3:1101:16858:25563#GTGAAA 163 5 19275940 255 1S65M24S = 19275940 65 GCCTTTTGAGACAATACAAATCAAAATATTTACAGAGATAAGGCAGAATCAAACTACATTAAGGAGGGTCTGAGATCGGAAGAGCGTCGT bbbeeeeegggggiiiiiiiiiiiiiiiiiiiiihiiiiiiiiiiiiihihiiiiiiiiihiiiiiiidggggggeeeeccccccccccc NH:i:1 HI:i:1 AS:i:124 nM:i:2 FCC1GLHACXX:3:1101:16858:25563#GTGAAA 83 5 19275940 255 19S65M6S = 19275940 -65 CGTGTGCTCTTCCGATCTGCCTTTTGAGACAATACAAATCAAAATATTTACAGAGATAAGGCAGAATCAAACTACATTAAGGAGGGTCTG cdddeeeegggihhhiiiiiihhfhiihghiihgiiihghiiiiiiiiiiihiiiiiiiiiiiiiiiiiiihhgiiigggggeeeeebbb NH:i:1 HI:i:1 AS:i:124 nM:i:2 FCC1GLHACXX:3:1101:16918:25584#GTGAAA 99 14 81019100 255 90M = 81019191 181 TTGTACCAGTTATCAAACTGTGTTTTGATGGGATAGAGATTGATATTTTGTTTGCAAGATTAGCACTGCAGACTATTCCAGAAGACTTGG bbbeeeeeggggghiiiiiiehdghiifhhiifghiegfhhhihiiiiiigiihifhihhhiiiiiiiiiiiiiiiihgggfggeee_cd NH:i:1 HI:i:1 AS:i:176 nM:i:1 FCC1GLHACXX:3:1101:16918:25584#GTGAAA 147 14 81019191 255 90M = 81019100 -181 CTTAAGAGATGACAGTCTGCTTAAAAATTTAGATATAAGATGTATAAGAAGTCTTAACGGTTGCAGGGTAACCGATGAAATTTTACATCT ddddddeeedeeeggggihdeiiiiiiiiiiihiihiiihhiihhhhiiihhihiihihhhiiiiiiiiiiiiiiiigggggeeeeeab_ NH:i:1 HI:i:1 AS:i:176 nM:i:1
Nicolas
Comment