Hello readers ,
I will start with the caveat that I am a newbie fumbling along the process of teaching myself how to analyse my Tru-seq data.
I tried excising the below mentioned adapter and the output has dwindled to ~20% of the original reads. This seems erroneous, I did not allow for any wiggle room with mis-matches. Is this too stringent? Or is there a wholesale error in the way i went about things? What happens to all the non-clipped reads?
Thanks
Info: Clipping Adapter: CGATGT
Min. Length: 15
Non-Clipped reads - discarded.
Input: 36838900 reads.
Output: 5341173 reads.
discarded 1539984 too-short reads.
discarded 127004 adapter-only reads.
discarded 29709745 non-clipped reads.
discarded 120994 N reads.
I will start with the caveat that I am a newbie fumbling along the process of teaching myself how to analyse my Tru-seq data.
I tried excising the below mentioned adapter and the output has dwindled to ~20% of the original reads. This seems erroneous, I did not allow for any wiggle room with mis-matches. Is this too stringent? Or is there a wholesale error in the way i went about things? What happens to all the non-clipped reads?
Thanks
Info: Clipping Adapter: CGATGT
Min. Length: 15
Non-Clipped reads - discarded.
Input: 36838900 reads.
Output: 5341173 reads.
discarded 1539984 too-short reads.
discarded 127004 adapter-only reads.
discarded 29709745 non-clipped reads.
discarded 120994 N reads.
Comment