On 09/14/2010 09:27 PM, Kunbin Qu wrote:
> Hi,
>
> I received the following error when I tried to read some fastq in and
> generate QA report. Could anybody help me? Thanks.
>
> -Kunbin
>
>
> [srp101]more tmp2
> @SEQUENCER01_0007:1:1:1066:13331#0/1
> CAGCTANCTGCGTTCTTCATCGACGCACGAGCCGAGTATTAATGTGAATTG
> +SEQUENCER01_0007:1:1:1066:13331#0/1
> fdfffcBccccccccfffffffeffffffcfffffedcfcffffddedfdd
> @SEQUENCER01_0007:1:1:1066:8699#0/1
> CTTACCNCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCAC
> +SEQUENCER01_0007:1:1:1066:8699#0/1
> cc^ccaBV]]ba_^Zc^cbaa`c`cL^```cb\ccc^aaaaa^aabba`bb
> @SEQUENCER01_0007:1:1:1066:20185#0/1
> GCCACANACACCTGATTATCAACAGCCCGGCTTCGCTGAAGTAACTCCCAA
> +SEQUENCER01_0007:1:1:1066:20185#0/1
> fffffbBbbbcccccfffffefffffffffeffffffffefffffdefffd
> [srp101]
>
>
>> s6<-readFastq("./", "tmp2")
>> q6<-qa(s6)
> Error: UserArgumentMismatch
> 'lane' must be 'character(1)'
see
?"qa,ShortReadQ-method'
it wants to be able to record which lane the data comes from, so
q6 <- qa(s6, "lane6tmp2")
or whatever is appropriate.
Martin
>
>
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> 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_1.6.2 Rsamtools_1.0.1 lattice_0.18-8
> [4] Biostrings_2.16.7 GenomicRanges_1.0.1 IRanges_1.6.8
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2
>>
>
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