Dear Martin,
I use nFilter to filter out the sequences which contain any "N",
following is my codes:
> # read the fastq file
> fq<-readFastq("/Users/wei/Desktop/Originaldata",pattern="Bic.txt")
> # filter for N containing reads
> filt<-nFilter()
> fq<-fq[filt(fq)]
> # write the out
> writeFastq(fq,file="/Users/wei/Desktop/Originaldata/bicfiltered.txt")
After I got the filtered fastq file:
>readFastq("/Users/wei/Desktop/Originaldata", "bicfiltered.txt")
Error in .local(dirPath, pattern,...) :
ShortRead internal: too many 'snap' entries
My sessioninfo():
R version 2.10.1 (2009-12-14)
x86_64-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.4.0 lattice_0.17-26 BSgenome_1.14.2
Biostrings_2.14.12 IRanges_1.4.11
loaded via a namespace (and not attached):
[1] Biobase_2.6.1 grid_2.10.1 hwriter_1.1 tools_2.10.1
Many thanks!
Wei
On 4/4/10 10:31 PM, Martin Morgan wrote:
On 04/04/2010 11:55 AM, Yanwei Tan wrote:
Hi Ramzi Temanni,
I met the same problem with you when running shortread. As Martin
mentioned, there is one new line missing after the last file record. How
did you fix this problem? I do not know how to add a new line after the
last line. My data is fastq file, I just filtered the reads which
contain N by using the nFilter function in shortread package.
In off-list email you said
I used ShortRead package to filter the data and then saved as fastq
file. But when I run the qa function again there is error in
.local(dirPath, pattern, ...):> > ShortRead internal: too many
'snap' entries.
It is hard to follow what you are trying to accomplish. Please paste
short code to illustrate. Use data files from ShortRead, so that your
code is reproducible by others. Include the output of sessionInfo() so
that it is clear which version of software you are using. Perhaps after
example(readFastq)
you do
rfq
class: ShortReadQ
length: 256 reads; width: 36 cycles
file = tempfile() # a file to save output
noNrfq = rfq[nFilter()(rfq)]
writeFastq(noNrfq, file)
qaresult = qa(dirname(file), basename(file), type="fastq")
? But what is the problem? Note also that it is not necessary to write
the fastq file to disk,
qa(list(noNrfq=noNrfq))
class: ShortReadQQA(9)
QA elements (access with qa[["elt"]]):
readCounts: data.frame(1 3)
baseCalls: data.frame(1 5)
readQualityScore: data.frame(512 4)
baseQuality: data.frame(94 3)
alignQuality: data.frame(1 3)
frequentSequences: data.frame(50 4)
sequenceDistribution: data.frame(3 4)
perCycle: list(2)
baseCall: data.frame(141 4)
quality: data.frame(341 5)
perTile: list(2)
readCounts: data.frame(0 4)
medianReadQualityScore: data.frame(0 4)
This is my sessionInfo()
sessionInfo()
R version 2.10.1 Patched (2010-03-27 r51570)
x86_64-unknown-linux-gnu
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=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.4.0 lattice_0.18-3 BSgenome_1.14.2
Biostrings_2.14.12
[5] IRanges_1.4.16
loaded via a namespace (and not attached):
[1] Biobase_2.6.1 grid_2.10.1 hwriter_1.2 tools_2.10.1
Many thanks in advance!
Wei
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--
Yanwei Tan
Institute of Neurobiology
1.OG, AG Bading
Im Neuenheimer Feld 364
University of Heidelberg
69120 Heidelberg
Germany
Tel:+49-6221-548319
Fax:+49-6221-546700
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