Dear all,
We recently submitted RNA-seq samples for sequencing to a local facility (20 cancer samples, 20 controls), where for each sample we sequenced approximately 100 million paired end 50 bp reads. However, after sequencing we found that several samples after sequencing only contained 6 million sequenced reads and others 50-80 million reads. Only about 5 samples had 90 million reads and above, with one sample having 180 million reads.
I am not sure what to make of this. There were some concerns regarding the RNA quality, of some of the samples, but I am not sure if that could lead to such low output. Our contact at the facility seems to suggest it is the RNA-quality, but I wanted to ask you experts just to be sure.
The fastQC analysis on the sequences do not show any significant issues in terms of quality, however it appears the filtering may be occuring during or just after the sequencing itself. If anyone has any ideas I would be much appreciative.
We recently submitted RNA-seq samples for sequencing to a local facility (20 cancer samples, 20 controls), where for each sample we sequenced approximately 100 million paired end 50 bp reads. However, after sequencing we found that several samples after sequencing only contained 6 million sequenced reads and others 50-80 million reads. Only about 5 samples had 90 million reads and above, with one sample having 180 million reads.
I am not sure what to make of this. There were some concerns regarding the RNA quality, of some of the samples, but I am not sure if that could lead to such low output. Our contact at the facility seems to suggest it is the RNA-quality, but I wanted to ask you experts just to be sure.
The fastQC analysis on the sequences do not show any significant issues in terms of quality, however it appears the filtering may be occuring during or just after the sequencing itself. If anyone has any ideas I would be much appreciative.
Comment