Dear all,
I am very new to the NGS world and my question might seem stupid.
In order to train using RNA-seq data, I downloaded the datasets coming from the paper by Marioni et al (2008) (see http://genome.cshlp.org/content/18/9/1509.full) where they compare the respective merits of affymetrix microarrays vs RNA sequencing.
I decided to apply tophat on this tool in order to do the mapping.
This dataset is composed of 2 sets of short reads of size 36 nucleotides (2 lanes for the sequecing of the kidney transcriptome as well as 2 lanes for the liver).
I used these commands :for the kidney and the liver respectively :
The problem is that I never get any junction found and I don't understand why.
E.g. : this is the content of the file log/reports.log
Any idea? Thanks a lot to all of you!
Sylvain
I am very new to the NGS world and my question might seem stupid.
In order to train using RNA-seq data, I downloaded the datasets coming from the paper by Marioni et al (2008) (see http://genome.cshlp.org/content/18/9/1509.full) where they compare the respective merits of affymetrix microarrays vs RNA sequencing.
I decided to apply tophat on this tool in order to do the mapping.
This dataset is composed of 2 sets of short reads of size 36 nucleotides (2 lanes for the sequecing of the kidney transcriptome as well as 2 lanes for the liver).
I used these commands :for the kidney and the liver respectively :
Code:
tophat --segment-length 12 -p 11 -o kidney_out $BOWTIE_INDEXES/complete_hg19_reference /data/datasylvain/marioni/kidney_2runs_1.fastq,/data/datasylvain/marioni/kidney_2runs_2.fastq tophat -p 11 --segment-length 12 -o liver_out $BOWTIE_INDEXES/complete_hg19_reference /data/datasylvain/marioni/liver_2runs_1.fastq,/data/datasylvain/marioni/liver_2runs_2.fastq
E.g. : this is the content of the file log/reports.log
Code:
tophat_reports v1.3.2 (2689) --------------------------------------- [samopen] SAM header is present: 93 sequences. Loaded 0 junctions Reporting final accepted alignments...done. Printing junction BED track...done Printing insertions...done Printing deletions...done Found 0 junctions from happy spliced reads
Sylvain
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