mw55309
commented
7 years ago Hey
Can you run sessionInfo() and post the results?
Also, which version of poRe are you using?
Cheers Mick
Open NathanielLegall opened 7 years ago
mw55309
commented
7 years ago Hey
Can you run sessionInfo() and post the results?
Also, which version of poRe are you using?
Cheers Mick
I'm having a bit of trouble extracting the metadata from our 1D reads. I suspect that this might be a format issue but I'm a newbee so help would be appreciated.
I've tried both the new and old formats referred to in 03_Run_QC.md...
BG_3 <- read.essential.info(newbc2) Warning message: NAs introduced by coercion plot.length.histogram(BG_3) Bg_4 <- read.fast5.info(newbc2, path.t="/Analyses/Basecall_1D_000/", path.c="/Analyses/Basecall_1D_000/") Warning message: NAs introduced by coercion plot.length.histogram(BG_4) Error in plot.length.histogram(BG_4) : object 'BG_4' not found
..but neither appear to work and give the error 'NAs introduced by coercion'. The error doesn't come up when I try it with the test data...
newbc2 <- system.file("/extdata/f5/new_bc", package="poRe") lambda <- read.fast5.info(newbc2) max(lambda$tlen) [1] 16387
...which is why I think that it might a formatting issue since ONT appear to keep changing the .fast5 file formatting.
Update: I've changed the files that poRe is looking at to files that have definitely been base called. I still received the warning message: NAs introduced by coercion after running read.fast5.info but it is taking a while to run plot.length.histogram. Will update again with result.