User: danova_fr

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danova_fr20
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Andorra
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2 years, 5 months ago
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Posts by danova_fr

<prev • 13 results • page 1 of 2 • next >
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Answer: A: ShortRead with large fastq files
... Thanks for answers. I will follow your advice and work with 1  cycle at a time.   Best, david   ...
written 2.5 years ago by danova_fr20
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Answer: A: ShortRead with large fastq files
... Thanks for the update. What i´m trying to achieve here is ( so I might be wrong the way i do it) is to compute the quantile at each cycle across all reads. This is working pretty wall with bacterial genomes using 16s amplicons . Now working with higher datasets (metagenomics samples doing shotgun s ...
written 2.5 years ago by danova_fr20
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Answer: A: ShortRead with large fastq files
... Ok tried I have tried the following: f <- FastqStreamer(file, 100000) #chunks of 100000 allqual <- list() i=1 while (length(fq <- yield(f)) ) { chunkqual <- as(quality(fq), "matrix") allqual[[i]] <- chunkqual i = i+1 } close(f) qual <- do.call(rbind,allqual) #quantile qt & ...
written 2.5 years ago by danova_fr20
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Answer: A: shortread with large fastq files
... > sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=ca_AD.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=ca_AD.U ...
written 2.5 years ago by danova_fr20
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ShortRead with large fastq files
... HI , I have a problem getting quality scores for the following large file.   My first step is to check the quality  to generate some stats for each fastq file, however it seems that i cannot allocate enough memory even though i have enough memory (10Gb). > fq class: ShortReadQ length: 243772 ...
shortread written 2.5 years ago by danova_fr20
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Answer: A: gcContent error with shortread
... great, thanks so much,   david   ...
written 2.5 years ago by danova_fr20
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Answer: A: gcContent error with shortread
... Sorry, Got it from the manual. gcContent <- function(x) { abc <- alphabetFrequency(sread(x), baseOnly=TRUE) gcPerRead <- rowSums(abc[,c("G", "C")]) wd <- unique(width(sread(x))) tabulate(1 + gcPerRead, 1 + wd) }     tabulate(1 + gcPerRead, 1 + wd) seems to returning the prev ...
written 2.5 years ago by danova_fr20
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gcContent error with shortread
... I´m processing a fastq file of reads that have already paired. Trying to get the GC content i get this error ??? > fq <- readFastq(file) > fq class: ShortReadQ length: 50545 reads; width: 79..503 cycles > gc <- gcContent(fq) Warning messages: 1: In if (nbins > .Machine$integer.ma ...
shortread written 2.5 years ago by danova_fr20
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Answer: A: ShortRead trim sequence at specific position
... Hi, following the example above there is something i don´t understand trimPos <- apply(pe, 1, function(x) sum(cumsum(x) < 1))   # Trim when pe <1 # My matrix is transposed but it does the work nicely > mean(trimPos) 277.3139 Ok so the mean trim position for all reads of my fil ...
written 2.6 years ago by danova_fr20 • updated 2.6 years ago by Martin Morgan ♦♦ 20k
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Answer: A: ShortRead trim sequence at specific position
... Great Martin, Works well. As for the low-quality bases if they are located at the 5´end of the sequence  I will remove them before trimming ends. In fact the trimming 3´end is a second filtering in my case.       ...
written 2.6 years ago by danova_fr20

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