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Old 07-11-2014, 12:02 PM   #6
kmcarr
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Location: USA, Midwest

Join Date: May 2008
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Quote:
Originally Posted by pengchy View Post
Thank kmcarr and blancha's reply.

More question:
When I use the fastq with the base quality like this:
Code:
@FCC22UBACXX:2:1101:1463:2233#ACACGCGG
TGGTCTTCTAAATATTGTCTGAGGGCTCCGTAAGCCTGTGTTTTAGCAC
+
@@@BDEFFHFF<FGHIHCCIHGEFIIIGGGGGI;B?GHHCBFGIIHIII
the output bam will be like this:
Code:
FCC22UBACXX:2:2112:11384:88500#ACACGCGG 0       AF024514.1      14      50      49M     *       0       0       ATATTGCTTCTATTTCGGTTTTGTTCAAGCGTTGACCGTTGCAGGCGCT     %$%(((((*****++++"(*+++*+++++++++++++++++++++++++       AS:i:-4 XN:i:0  XM:i:2  XO:i:0  XG:i:0  NM:i:MD:Z:17A1A29     YT:Z:UU NH:i:1
FCC22UBACXX:2:1313:19247:88511#ACACGCGG 0       AF024514.1      15      50      49M     *       0       0       TATTGCTTCTATTTCGATTTTGTTCAAGCGTTGACCGTTGCAGGCGCTT     $$$(((((&((&(*))'%(**+&(*++*&)''')&)+++%()))'&()%       AS:i:-2 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:MD:Z:18A30       YT:Z:UU NH:i:1
Is it normal? I have used this bam file to call snp, none snp has been found, while several sites can be manually detected. Is it caused by this base quality?
Pengchy,

Again, you are showing us different reads from the FastQ file and from the BAM file. To best understand what is going on you really need to show us the FastQ record and the BAM record for the SAME read(s).

Do you know what the quality encoding was in your input FastQ? You really need to have this information before you start your analysis.

What version of Tophat are you using?

When you ran Tophat did you use a command line parameter to tell Tophat what q-score encoding was used for the input FastQ or did you leave it as default?
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