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junchaoshi / sports1.1

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
GNU General Public License v3.0
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Overlapping between different annotation? #15

Closed xiaoyunguo closed 3 years ago

xiaoyunguo commented 3 years ago

Hi,

Thank you so much for prompt reply to my previous questions. Really appreciate it. I have more questions about interpreting the output from sports:

Thank you so much for your help!

--------- following is the classes in the summary.txt file in my case---

GtRNAdb-mature-tRNA_Match_Genome GtRNAdb-mature-tRNA_5_end_Match_Genome GtRNAdb-mature-tRNA_3_end_Match_Genome GtRNAdb-mature-tRNA_CCA_end_Match_Genome GtRNAdb-mature-tRNA_Unmatch_Genome GtRNAdb-mature-tRNA_CCA_end_Unmatch_Genome mitotRNAdb-mature-mt_tRNA_Match_Genome mitotRNAdb-mature-mt_tRNA_3_end_Match_Genome mitotRNAdb-mature-mt_tRNA_CCA_end_Match_Genome mitotRNAdb-mature-mt_tRNA_Unmatch_Genome mitotRNAdb-mature-mt_tRNA_CCA_end_Unmatch_Genome

junchaoshi commented 3 years ago

_Is there overlapping between different classes? for example in output xxx.summary.txt, I saw the following classes for tRNA. Are reads counted in tRNA_5_end (and other ends) also counted in the tRNA_MatchGenome class? Yes, one tsRNA can be annotated as tRNA 5 end and genome matched. These two kinds of annotation are independent.

_The output pdf files shows the percentage of each type of tRNA in a pie chart, how the tRNA percentage is calculated? (5-end, 3-end, and CCA-end divided by the tRNA_match_genome plus tRNA_unmatchgenome? are mitotRNA also included in the calculation? Yes, the percentage of each subtype of tsRNAs is based on all kinds of tsRNAs, including genome matched and genome unmatched.