Entering edit mode
7.8 years ago
Hi,
I'm hoping someone can give me some insight as to what may have gone wrong during my PGM run.
I have for 4 samples , 330 M (Total bases), 53% ISPs loading , 2,391,670 Total reads, 99% enrichment, but 49% polyclonal and 19% unaligned read .
Only for one sample i have 1,928,790 mapped reads, for the other samples I have very low mapped reads.
These are samples from FFPE but my amplicons are long 120 bp. I think that the unaligned reads are the longer than the aligned. What is due a high percentage of unmapped reads ? For the 49% of polyclonal ISPs , i think could be the reagents of OT that are expired. Thanks
While someone else may be along with Ion specific advice have you tried to take some of the unaligned reads and check them at NCBI Blast to see if they are what you expect them to be? This is always a good step to start with when you have unaligned data showing up in your samples.
I assume you may have used the built-in aligner (TMAP?) from torrent server. Have you tried something else in addition?
Adding to what genomax2 said, you could also screen for contaminants using Kraken.