Hi Dario --
On 8/25/2010 12:00 AM, Dario Strbenac wrote:
Hello,
I've updated my ShortRead and IRanges packages recently and the qa function
doesn't
I'm guessing that you mean you updated from ShortRead 1.6.0. to 1.6.2.
There don't look like there are code changes that would cause problems
with this...
work for me anymore. It spends a couple of minutes processing, then fails with
an error :
str(path)
chr "C:/Users/dario/Documents/Garvan/rawData/seq/Ramaciotti/25-03-2010/s_1_1"
dir(path)
[1] "12627LN-FFPET_MBD2IP_1.Rdata" "12627LN-FFPET_MBD2IP_1.wig.gz" "12627LN-FFPET_MBD2IP_1_GR.Rdata"
"mapping.log" "s_1_sequence.fastq.gz" "s_1_sequence.uniq.map.gz"
QAfastq<- qa(path, "fastq.gz", "fastq")
Error in stop(msg, " ", errors, domain = NA) :
no function to return from, jumping to top level
Error in slot(object, ".srlist") :
cannot get a slot (".srlist") from an object of type "NULL"
In addition: Warning message:
UnspecifiedWarning
elements: 1
UnspecifiedError: qa(readFastq(dirPath, pattern, ...), pattern, verbose =
verbose)
error in evaluating the argument 'dirPath' in selecting a method for function
'qa'
does
fl = list.files(path, "fastq.gz", full=TRUE)
return something sensible (just the path to s_1_seqeunce.fastq.gz)?
Does
.Call(ShortRead:::.read_solexa_fastq, fl, TRUE)
return a list containing the sequences, ids, and qualities? If not, then
there are problems parsing the fastq file. The parser expects the reads
/ qualities to occupy a single line each, and the qualities to be
encoded. Is that the case for these reads? Also, how many and what
length are the reads supposed to be?
Martin
sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-pc-mingw32
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.6.2 Rsamtools_1.0.0 lattice_0.18-5
Biostrings_2.16.0 GenomicRanges_1.0.7 IRanges_1.6.15
loaded via a namespace (and not attached):
[1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2 tools_2.11.0
Could this be a bug in the function ?
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
