While running HTSeq, which option is recommended to use among -m union, -m intersection-empty, and -m intersection-strict?
The below is one of the results I've got. Would you please give me a tip about with which data I will have to analyze in the next step? I am thinking of adopting DESeq or EdgeR.
CASE1: -m union
no_feature 4152
ambiguous 391
too_low_aQual 0
not_aligned 0
alignment_not_unique 4110
CASE2: -m intersectioin-nonempty
no_feature 4223
ambiguous 249
too_low_aQual 0
not_aligned 0
alignment_not_unique 4110
CASE3: -m intersection-strict
no_feature 7797
ambiguous 221
too_low_aQual 0
not_aligned 0
alignment_not_unique 4110
The below is one of the results I've got. Would you please give me a tip about with which data I will have to analyze in the next step? I am thinking of adopting DESeq or EdgeR.
CASE1: -m union
no_feature 4152
ambiguous 391
too_low_aQual 0
not_aligned 0
alignment_not_unique 4110
CASE2: -m intersectioin-nonempty
no_feature 4223
ambiguous 249
too_low_aQual 0
not_aligned 0
alignment_not_unique 4110
CASE3: -m intersection-strict
no_feature 7797
ambiguous 221
too_low_aQual 0
not_aligned 0
alignment_not_unique 4110
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