Hi,
We recently performed a small RNAseq for the first time at our institute (and NGS core) and unfortunately the quality of the reads is not ideal. However, it would be nice if I can still get something out of the data...
Therefore, I was wondering if I could change the tophat options used for alignment of the reads (at the moment the default options are used), i.e.if there are certain parameters specific for small RNA analysis?
Or is there anything else to consider? (after tophat I'm only counting the reads and compare these between the different samples, so tophat seems to be the crucial step for the analysis).
Thanks in advance,
Jeannine
We recently performed a small RNAseq for the first time at our institute (and NGS core) and unfortunately the quality of the reads is not ideal. However, it would be nice if I can still get something out of the data...
Therefore, I was wondering if I could change the tophat options used for alignment of the reads (at the moment the default options are used), i.e.if there are certain parameters specific for small RNA analysis?
Or is there anything else to consider? (after tophat I'm only counting the reads and compare these between the different samples, so tophat seems to be the crucial step for the analysis).
Thanks in advance,
Jeannine
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