Custom Regular Expression Causes Extraction Failure

[DarioS]

I used the regular expression ACC(.{20,21})GTTTT and received the error "The entered FASTQ regular expression did only work for 0 to 0% of sequences within your FASTQ files." Using grep directly demonstrates that the regular expression I tried to use is correct:

$ zgrep -E 'ACC(.{20,21})GTTTT' treatedA.fastq.gz | head -n 3 -
ATACACGATCTCTTGTGGAAAGGACGAAACACCGAGTATCTAATTATAGCCTTCGTTTTAGAGCTAGAAATAGCA
ATCGATTCCTTGGTTCTTGTGGAAAGGACGAAACACCAGCGCCGACGTGCTCACAGTGGTTTTAGAGCTAGAAAT
ATACACGATCTCTTGTGGAAAGGACGAAACACCGCAGATGGGCGGACAATTTCAGTTTTAGAGCTAGAAATAGCA

Choosing Standard for LenticrispV2 fails with "The entered FASTQ regular expression did only work for 1.1 to 1.64% of sequences within your FASTQ files." although it doesn't fail if I use it in a new application session without having entered a custom error-raising regular expression first. The only way to continue analysis is to restart the application and choose LenticrispV2 the first time. The extraction rate is then about 96%.

[jwinter6]

Hi,

just to make it clear:

• it works if you select the default setting in the beginning
• once you add a custom regular expression (the one above), it fails (though it is the same regex)
• and if you then select one of the defaults afterwards, it does not work anymore?

One question:

• did you click the reset button between in between?

Seems like there is a glitch in the reactive handling - thanks for pointing this out. However I did not observe any issues with custom regular expressions before, but I will also check this.

Best Jan

[DarioS]

That summary describes the problem concisely.

I didn't click on the User Other Files button.

[jwinter6]

Hi, I am on it and it will be changed with the 1.16 release in a couple of days.

Best Jan