User: chapmandu2

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chapmandu220
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Posts by chapmandu2

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Comment: C: Using ShortRead (or other) to trim from pattern match onwards
... For completeness this is what I get with 1000 reads: system.time(polyApos_vmp <- vmatchPattern(paste0(rep('A',10), collapse=''),sread(fq4), fixed=TRUE)) user system elapsed 0.02 0.00 0.02 system.time(starts <- start(polyApos_vmp)) ### SLOW!!! user system elapsed 3.845 ...
written 19 months ago by chapmandu220
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Comment: C: Using ShortRead (or other) to trim from pattern match onwards
... Fantastic thanks Martin, I had forgotten about that.  I get a x10 speed boost on 1 milion reads > system.time(polyApos <- sapply(as.character(sread(fq3)), regexpr, pattern= paste0(rep('A',10), collapse=''), USE.NAMES = FALSE) %>% unlist()) user system elapsed 11.738 0.042 11.778 & ...
written 19 months ago by chapmandu220
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Comment: C: Using ShortRead (or other) to trim from pattern match onwards
... Thanks Martin.  I tried your method but although it worked fine on the example when I applied it to larger datasets (1M reads) it was slowed right down. What I ended up with was the below converting the reads to characters and then just doing a regexpr: match_pos <- unlist(sapply(as.character( ...
written 19 months ago by chapmandu220
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Using ShortRead (or other) to trim from pattern match onwards
... Apologies if this has been asked before, I've found several similar questions but nothing quite what I want... I am analysing some data from a 3'UTR-RNA-seq protocol.  In a 150bp NextSeq read, what often happens is that you get something like: 12bpAdapter---100bpRNA--15bpPolyA--20bpAdapter The 12 ...
shortread written 19 months ago by chapmandu220 • updated 19 months ago by Martin Morgan ♦♦ 20k

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