Documentation about strand-sensitive anaylsis

[visze]

There are a lot of questions about analysing stand specificity. So it might be a good idea to add some documentation about this.

Technically it is not possible to analyse stand specificity. Mapping is not possible to regions that are identical (in terms of forward, reverse, complement and reverse complement).

When analysing strand specificity you have to add by design different nucleotides at the beginning and and at the end so that mapping (BWA mem) is able to discriminate between the sequences. When using the restriction enzyme free approach the two 15bp adapters can be used for that. But they have to be in the design file and these adapters should not be trimmed in reads.

[superjingjing]

1. I agree, I usually add primers back to both sides and then map with BWA .
2. Another way is to use bowtie2 strand-sensitive mode.

[visze]

Do you have experience with the strand sensitive mode of bowtie? Is it worth to implement it?