Thank you for "-Q 33" tip. Very useful !
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I got another problem except "#".
fastx_quality_stats: Invalid quality score value (char 'J' ord 74 quality value 41) on line 8.
line8: @CCFFFFFDDFHHIJIIJJGIIGIGJGEEHIIIGG>FHGJIGHIGGIIJGIH9DHHGGCCHE7?B?3;(;=AB9@@@CDCA;3?<A##############Comment
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You need to upgrade to the latest version of FASTX Toolkit (verion 0.0.13). FASTX Toolkit has several functions which check the validity of the data as it is processing it; one of these checks is to see if the quality values fall within a reasonable range. This range used to be defined as -15 to 40. The latest version of the Toolkit expands this range to -15 to 93.Originally posted by zhouzf View Post
Older versions of FASTX Toolkit do not work with the latest version of the Illumina basecalling software. In the latest version of Illumina's software they allow a maximum Q-Scores of 41 ("J"). If you are using an older version of FASTX Toolkit it will report an error at the first "J" it encounters. Upgrade to FASTX Toolkit 0.0.13 and your problem will be solved.Comment
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Still not documented
3 years later, the -Q 33 option is still needed and still not documented.Comment
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The best solution in my opinion is to use the latest FASTX version, which accommodates multiple fastq formats. The only drawback is that you have to compile from source, but it's standard ./configure && make && make install. Make sure to install libGtextUtils first. Both are available at http://hannonlab.cshl.edu/fastx_toolkit/download.html. If you install libGtextUtils in a non-standard location, such as $HOME/bin, be sure to add "export PKG_CONFIG_PATH=$HOME/bin/lib/pkgconfig" to .bashrc. Also, whatever directory you install FASTX into, the executables will be put in a bin directory underneath it, so for me it was $HOME/bin/bin, which I added to $PATH.Comment
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I agree #19's pointComment
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