strand information for MoSEA not using SUPPA2 events

[JamalEH]

Dear team, May this email finds you all fine.

I have a question related to using MoSEA using coordinates from a tool different than SUPPA2. my question is should I provide the strand information when extracting the sequences ? My bed file looks lik the following: chr18 63127035 63128759 BCL2_E1 chr18 63123346 63127034 BCL2_E2 chr18 63126835 63127035 BCL2_U1 chr18 63126834 63127034 BCL2_U2

Providing the above file to I got the sequences. When I scan the sequences for the occurrence of the RBP binding motif i got something like: #pattern name sequence name start stop strand score p-value q-value matched sequence HNRNPL_00091 BCL2_E1 794 800 + 8.13415 0.000743 ACACAAT HNRNPL_00091 BCL2_E1 1260 1266 + 10.0671 7.11e-05 ACACGAA HNRNPL_00091 BCL2_E2 87 93 + 10.0549 0.000159 ACACAAA HNRNPL_00091 BCL2_E2 1122 1128 + 9.96951 0.000413 ACACAAG HNRNPL_00091 BCL2_E2 1426 1432 + 8.2378 0.000536 ACACCAC HNRNPL_00091 BCL2_E2 1877 1883 + 7.56098 0.000996 ACACAGA

Looking at the strand column the tool reports a sequence on the positive strand, while my gene BCL2 is on the reverse strand "ensembl location: Chromosome 18: 63,123,346-63,320,128 reverse strand". I'm using the hg38 genome assembly to extract sequences.

I will be very thankful if you can help me to fix this issue. Thank you so much in advance! Kind regards, Jamal.