We have obtained a lot of RNA-seq reads from HiSeq with 100bp in length. We are trying to align them to a splice junction database which only contain sequences that are 62bp in length. Is this possible? Are there any parameter values that need to be tweaked? Would soft clipping automatically mark both hanging 5' and 3' read fragments?
Hope some BWA guru can answer the above questions. Thanks!
Hope some BWA guru can answer the above questions. Thanks!
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