how to get the quality score system information from the reads
1
0
Entering edit mode
wang peter ★ 2.0k
@wang-peter-4647
Last seen 10.3 years ago
i remember the shortread package can identify the read score system is phred+33 or 64 if i use reads <- yield(inFh) or reads <- readFastq(fastqfile);\ how can i get that information from the reads? thank you -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253
ShortRead ShortRead • 1.1k views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 5 months ago
United States
On 11/8/2012 4:18 PM, wang peter wrote: > i remember the shortread package can identify the read score system is > phred+33 or 64 > > if i use > > reads <- yield(inFh) > or reads <- readFastq(fastqfile);\ > > how can i get that information from the reads? quality(reads) returns an object that displays either class: SFastqQuality in which case the reads are 'Solexa' (phred + 64) encoded or class: FastqQuality in which case they are phred + 33 encoded. ?readFastq contains information on this. Martin > > thank you > -- Dr. Martin Morgan, PhD Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
ADD COMMENT
0
Entering edit mode
thank u very much for your help but i would like to know how to extract the string SFastqQuality or FastqQuality
ADD REPLY
0
Entering edit mode
can i use data.class(quality(reads)) shan
ADD REPLY
0
Entering edit mode
On 11/8/2012 5:25 PM, wang peter wrote: > can i use > data.class(quality(reads)) yes, or class(quality(reads)) or is(quality(reads), "SFastqQuality") > > > shan > -- Dr. Martin Morgan, PhD Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
ADD REPLY

Login before adding your answer.

Traffic: 451 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6