Dear All,
I have a question about paired-end Illumina Hiseq100 data. My fastq files have normal average quality, but Bowtie can only map about 10% of the reads. However, TopHAt maps around 80%. Does anyone know why this happens?
Also, when I display TopHat bam files in UCSC browser, I get left-hand reads colored blue and right-end reads-red. The same color scheme is used for single-end reads to show strand specificity. But paired-end reads in USCS browser have no visible strand indication. Or is it just that I do not see it?
When reads are assembled into transcripts by Cufflinks, each transcript is annotated to either "plus" or "minus" strand and it generally corresponds right with reference annotation. But some transcripts get "antisense" class codes (x) and I would like to check how many reads actually build them.
Does anyone know how to make paired-end reads look strand specific?
I have a question about paired-end Illumina Hiseq100 data. My fastq files have normal average quality, but Bowtie can only map about 10% of the reads. However, TopHAt maps around 80%. Does anyone know why this happens?
Also, when I display TopHat bam files in UCSC browser, I get left-hand reads colored blue and right-end reads-red. The same color scheme is used for single-end reads to show strand specificity. But paired-end reads in USCS browser have no visible strand indication. Or is it just that I do not see it?
When reads are assembled into transcripts by Cufflinks, each transcript is annotated to either "plus" or "minus" strand and it generally corresponds right with reference annotation. But some transcripts get "antisense" class codes (x) and I would like to check how many reads actually build them.
Does anyone know how to make paired-end reads look strand specific?
Comment