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Old 07-10-2014, 11:10 PM   #1
pengchy
Senior Member
 
Location: China

Join Date: Feb 2009
Posts: 116
Default base quality encoding changed after tophat2 mapping

fastq
Code:
@FCC22UBACXX:2:1101:1463:2233#ACACGCGG/1
TGGTCTTCTAAATATTGTCTGAGGGCTCCGTAAGCCTGTGTTTTAGCAC
+
___acdeegee[efghgbbhgfdehhhfffffhZa^fggbaefhhghhh
after tophat2 mapping, the fastq base quality was changed into:
Code:
FCC22UBACXX:2:1115:5744:8409#ACACGCGG   256     EQ110773        344     3       49M     *       0       0       ATAAAACCCGACAAAAGCTGTTCGGAAAGCTCTACGGGCTCGACCGGCA     CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJHFDDD       AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:MD:Z:49  YT:Z:UU NH:i:2  CC:Z:EQ123351   CP:i:3745       HI:i:0
also, if the input was solexa-quality, the base quality in the output bam will be 0-40, which will influence the downstream analysis.

Any idea?
Thank you.
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