Chang Ye
Chang Ye
Hi @marcelm, I have a similar problem, but it is more common one. Given a sequence with 5' adapter, eg **ALONGADAPTOR**sequence, if sequence is low quality in the end, or...
Hi @sfchen, I have also found that fastp can not deal with "read through" reads correctly. A diagram from Trimmomatic:  Read1 fastq file: ``` @K00159:45:H4W76BBXX:5:1105:20791:9167 1:N:0:CAACTA AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAGAGCACACGTCTGAACTCCAGTCACCACGATATCTCGTATGCCGTCATCTGCCAGAAAAAAG + AAFFFJJ7JFFFJJJFAFJJJJJJJJFJJJFJJAFJJAJA-F7JJFFAJFJJJJJJJJJJ
fastq can not deal with some adapters in SE mode either. for example: ``` @K00159:45:H4W76BBXX:5:1103:11931:62171 1:N:0:CAACTA GAGGACGAGGAGATCGGGAAGAGCACACGTCTGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGAAAAAACAAAACACGCCTATCGCCGGCGAAGTCCGGAAACAAGCAAAACAAAAGTCCAACCGGGGGAGAGCCTAC + AAAFFFJ7JJJAFFFA-AJJJJJJJJJJJJJJJJJJJJJJJAJFJJJJJJJJJJJJJJJJJJJJJJJJFFJFJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJ-FAJJJFJA7FJJJJJJJJJJJJJJJJJJFFJJFJJFJFJF @K00159:45:H4W76BBXX:5:1103:19157:62277 1:N:0:CAACTA GAAAGTCGGAGATCGGGAAGAGCACACGTCTGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAGAACGGTGGTGCCCCGCTGGGAGAGGTTAACCACAACAAGAAAAATAAATGTCGCCACTGAGGCCAAC + AAFFFFJFJJJJJAFFJFJJJJJJJJAJJAJFJA
I think break lines in a **uniform way** for a long line will be better. > `black` formatter for python run in such way. Before: ```R ggplot(flow_df, aes(y = Freq,...
@lorenzwalthert I can't find enough of R language formatter implementation to illustrate this problem. You can do the formattting test of the following python code with two different tools. The...
@lorenzwalthert Thanks for the improvement, but the latest version of styler is still quite slow... ``` $ R --version R version 3.6.3 (2020-02-29) -- "Holding the Windsock" $ R -e...
I don't know much about the principles of styler, but I wonder if adding asynchronous programming can help, which is widely used in the formatter of other languages.
I suppose most of the functions in styler don't need to run sequentially, thus wrapping those functions by promises package in R might bring some improvement. Just in the same...
HI @bendichter For scatter plot, we also need clip_on=False, correct?