On 03/23/2011 04:07 PM, Martin Morgan wrote:
On 03/23/2011 03:58 PM, joseph wrote:
Hello
How would you fix a FASTQ file that gives the following error when
read with
readFastq()?
Other lanes from the same flow cell are imported fine with readFastq().
rfq = readFastq("~/myDir", pattern="reads.fq")
Error: Input/Output
file(s):
~/myDir/reads.fq
message: IncompatibleTypes
message: invalid class "ShortReadQ" object: some sread and quality widths
differ
you could read the file in
x = readLines('~/myDir/reads.fq')
split it into reads and qualities
rd = x[c(FALSE, TRUE, FALSE, FALSE)]
qual = x[c(FALSE, FALSE, TRUE, FALSE)]
oops, x[c(FALSE, FALSE, FALSE, TRUE)]
and ask which have different numbers of characters
which(nchar(rd) != nchar(qual))
Martin
head reads.fq
@GAII_0001:6:1:0:101#0/1
NCTCANCATTGTTTGGACGGAACAAAACCGGGGACAATCT
+GAII_0001:6:1:0:101#0/1
BX[_\B_VXGQQU]]]YTPMGWTZZTVQ_X[TGYPZG[WZ
@GAII_0001:6:1:0:123#0/1
NGTGANTCNGCTCATTGCGAGTTTTAACCTTTTCTCTATC
+GAII_0001:6:1:0:123#0/1
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@GAII_0001:6:1:0:168#0/1
NCCAGNCCCAGCAGCCCTTCCTTTTCCCTGCTTACCCTCA
[[alternative HTML version deleted]]
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