New to RNAseq, thus everything found seems interesting to me, and as well, strange to me.
I used TopHat mapping my mouse PE100 data to its reference genome and got about 85~90% mapped.
Then, I looked into those unmapped reads and found some reads look like this:CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCACACCTCAAAAAACACCCCAAAATAAAAATAACCGATCTGATTTAAAAATTAG
I found about 20, 000+ reads like the above one ( >40 C at the head) among total 30 M reads.
Is this usual? Or can we tell anything from these unmapped reads?
I used TopHat mapping my mouse PE100 data to its reference genome and got about 85~90% mapped.
Then, I looked into those unmapped reads and found some reads look like this:CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCACACCTCAAAAAACACCCCAAAATAAAAATAACCGATCTGATTTAAAAATTAG
I found about 20, 000+ reads like the above one ( >40 C at the head) among total 30 M reads.
Is this usual? Or can we tell anything from these unmapped reads?
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