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Old 05-13-2011, 05:16 PM   #21
SamH
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Default Isolated B's

Hi, hopefully I can revive this old thread for a little. I just got a big dataset from a HiSeq2000 machine at Berkeley, I'm not sure which version of the Illumina pipeline was used, but I do see single "B" qualities in some reads
i.e.


@HS1_0077:5:1101:1205:2082#0/1
NCCCCAAAGCATGATGTTTCCACCCCCATGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGACCGATATCGTATGCCGTCTTCCGC
+HS1_0077:5:1101:1205:2082#0/1
BTSTTV[VYYc_ac_cccccccc[YUYV_cBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@HS1_0077:5:1101:1231:2094#0/1
NTGTGGTATATATGCATGTAGTTACTTGGCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTCTCCACGATCTCCACACACACCCTCT
+HS1_0077:5:1101:1231:2094#0/1
BUPNUSSUUUcccac_c_ccccc_ccc_caBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB


SamH
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Old 05-14-2011, 12:38 AM   #22
maubp
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As discussed earlier in this thread, you can have lone B qualities (PHRED 2) in the quality string, and a trailing block of B markers as well. The second example here specifically copes this:
http://news.open-bio.org/news/2010/0...q2-trim-fastq/
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Old 08-29-2013, 06:25 AM   #23
NikTuzov
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Hi:

I have a question about the so-called Sanger format where Q can be in [0;93] represented by [!-~]. Since this is the set of all visible ASCII characters, then it looks like there is no symbol reserved for a missing value. Does it mean that specifying missing values for the quality of individual base pairs is impossible? If yes, why?
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Old 08-29-2013, 06:46 AM   #24
maubp
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Quote:
Originally Posted by NikTuzov View Post
Hi:

I have a question about the so-called Sanger format where Q can be in [0;93] represented by [!-~]. Since this is the set of all visible ASCII characters, then it looks like there is no symbol reserved for a missing value. Does it mean that specifying missing values for the quality of individual base pairs is impossible? If yes, why?
Yes, although in this case you could use PHRED quality 0 (and I recall some tools may use the upper bound 93 as a special value).

Why? None of the early technologies needed a missing value quality score.
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Old 08-29-2013, 07:01 AM   #25
NikTuzov
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Quote:
Originally Posted by maubp View Post
Yes, although in this case you could use PHRED quality 0 (and I recall some tools may use the upper bound 93 as a special value).
Thanks. I take it the encoding of missing values depends on the sequencer and it cannot be changed downstream. Therefore, I don't see how some downstream tool can use 93 as a missing value when it is not seen as such by the sequencing instrument.
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