????????????????

???????????????Sequencing By Synthesis??SBS????????Illumina HiSeq2500?????????????cDNA?????в?????????????????????Reads????????????????ЩReads??????????????Raw Data?????????????????????????Q30??Raw Data?????FASTQ???????????????????Raw Data????????FASTQ???????????????cDNA??????????Reads??
????FASTQ?????????????￡?

????FASTQ??????????
???????FASTQ?????????4?ж????????е???????????@???????????????б????ID???????????????????????????????????У???Reads??????????“+”????????????????????????????????Reads?????????????????????????????Reads?????г????????
???????????????
??????????????Quality Score??Q-score?????????Base Calling?????????????????????????Phred??????????????
????????У?P????????????????±???????????????????????????????????
??????1 ??????????????????????????????

???????????????????????????????????????????С?????磬????????????Q20???????100?????????1???????????????????????Q30???????1??000?????????1???????????Q40???10??000??????в???1???????????
???????????????λ??????????????Reads??в??????????????????????????????????????????????????????????

????????????????
??????????????????????Reads???λ????????????????????????????????????????????????λ?ò???????????????????????????????????????
????????????????
????FASTQ????в???Reads??????????ο?????????????б?????λcDNA?????????????????λ?á??????б??????????????????ЩReads????????????????????????????????????????????????￡?
????(1) ???????????????????У?
????(2) ????????????????????????????
???????????????е?????????????????????Reads?????????Clean Data??Clean Data?????FASTQ???????
??????????????????
?????????????????????????±??
??????2 ???????????????????

???????Samples??????????????????ID?????????Read Number??Clean Data??pair-end Reads???????????????Base Number??Clean Data????????GC Content??Clean Data GC????????Clean Data??G??C?????????????????%≥Q30??Clean Data?????????????30?????????????
??????????????ο??????????б??
???????Clean Reads????????ο?????????????б????????ο??????????????λ????????????????????е??????????????
????TopHat2???????Ч?????б???????????????Reads??????Bowtie????????????????Reads????????????????????????????????????????????Splicing Junction?????????????????????????????????????????Reads?????ο??????飬????????????????????
????????????????У???б????ο?????????????????????????????????????????????ο??????????Reads???Mapped Reads?????????????Mapped Data??