Graceful handling of zero-length reads?

[Danyang1111]

Hi, I am trying to generate quality plot, when I type:
plotQualityProfile(cutFs[1])
Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in density.default(qscore): 'x' contains missing values
How to deal with it?

[benjjneb]

What is the output when you run library(ShortRead);foo<-readFastq(cutFs[1])?

[Dianapthv]

Hi, i have the same problem:

plotQualityProfile(cutFs[1:2])
Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in density.default(qscore): 'x' contains missing values.

When I run library(ShortRead);foo<-readFastq(cutFs[1]) output looks like

print(foo)
class: ShortReadQ
length: 754907 reads; width: 0..200 cycles

[benjjneb]

@Dianapthv It looks like you have some reads that are length zero, which is causing this error. If you filter out reads below a reasonable minimum length that should be resolved. Or just work with the original data rather than the post-processing data that led to these zero-length reads.