Hi guys,
another problem to solve. I am running TopHat on some human cells samples I have submitted to our facility for RNAseq. The bioanalyzer values were great (all above RIN 8.5) and thus a library based exclusively on ribo depletion has been created.
I have multiplexed 4 samples in a lane (75bp, single-end) and obtained roughly 50 mil reads for each sample.
This is my TopHat summary:
Reads kept by tophat2 for mapping: 48777778
Reads discarded by tophat2: 321249
Number of unique reads that mapped: 5922988
Percentage of unique reads that mapped: 12.06%
I have used transcriptome for Tophat2...but I cannot understand why such a low mapping percentage (not the same across the samples, ranges across 12-40%).
Do you have any idea???
Other groups in our lab (doing polyA selection, on same cells, using same RNAseq pipeline) map almost 90% of the reads.
Help me please!!!
Thanks
Manu
another problem to solve. I am running TopHat on some human cells samples I have submitted to our facility for RNAseq. The bioanalyzer values were great (all above RIN 8.5) and thus a library based exclusively on ribo depletion has been created.
I have multiplexed 4 samples in a lane (75bp, single-end) and obtained roughly 50 mil reads for each sample.
This is my TopHat summary:
Reads kept by tophat2 for mapping: 48777778
Reads discarded by tophat2: 321249
Number of unique reads that mapped: 5922988
Percentage of unique reads that mapped: 12.06%
I have used transcriptome for Tophat2...but I cannot understand why such a low mapping percentage (not the same across the samples, ranges across 12-40%).
Do you have any idea???
Other groups in our lab (doing polyA selection, on same cells, using same RNAseq pipeline) map almost 90% of the reads.
Help me please!!!
Thanks
Manu