Closed CharlesJB closed 11 years ago
sebhtml
commented
11 years ago The tool assumes that there are 4 files for each group: R1, R2, R3, R4. This information is in the README.
A work-around for ChIP-Seq is to mv the R3 to R4 and to sym. link R2 to R3
R1
R2
R3 -> R2
R4 (old R3)
sebhtml
commented
11 years ago Paths to reproduce the problem on colosse:
/rap/nne-790-ab/Instruments/Illumina_HiSeq_1000_Hellbound/130131_SNL131_0070_AC1MMMACXX/SampleSheet.csv
/rap/nne-790-ab/Instruments/Illumina_HiSeq_1000_Hellbound/130131_SNL131_0070_AC1MMMACXX/Convert_binary_to_FastQ_1
CharlesJB
commented
11 years ago ??
On Fri, Apr 19, 2013 at 12:34 PM, Sébastien Boisvert < notifications@github.com> wrote:
/rap/nne-790-ab/Instruments/Illumina_HiSeq_1000_Hellbound/130131_SNL131_0070_AC1MMMACXX/SampleSheet.csv
/rap/nne-790-ab/Instruments/Illumina_HiSeq_1000_Hellbound/130131_SNL131_0070_AC1MMMACXX/Convert_binary_to_FastQ_1
— Reply to this email directly or view it on GitHubhttps://github.com/sebhtml/FastDemultiplexer/issues/1#issuecomment-16663558 .
sebhtml
commented
11 years ago At the moment, you need to do some symbolic links.
Create-R1-R2-R3-R4-Tree-from-R1-R2-R3-Tree.sh will do that for you.
Some sequencing runs produce only R1, R2 and R3 files.
Problematic lines:
[232] self.m_r4Files=[] [...] [256] self.m_reader4=FileReader(self.m_directory+"/"+self.m_r4Files[self.m_current]) [...] [271] return [self.m_reader1.getNext(), self.m_reader2.getNext(), self.m_reader3.getNext(), self.m_reader4.getNext()] [...] [369] outputDirectory.write(project,sample,lane,[sequenceTuple[0],sequenceTuple[3]])