[BioC] strand consistency with readAligned, coverage and transcriptsBy

[tefina]

Hi,

I have a question regarding consistency of strand.
Although reading the documentation and several tutorials I am not totally sure
if I have understood everything right.

Lets say you read in a fastq file from bowtie with readAligned.

x = readAligned("fastq-file", type = "Bowtie").

For each read you have the corresponding strand info.

If you then compute the coverage,

cov = coverage(x)

Is this the coverage on the + strand? Reads that aligned to the - strand are
reverse complemented and counted for the + strand?

Then you load a transcript database:

yeastDb = makeTranscriptDbFromBiomart(biomart = "ensembl", dataset =
"scerevisiae_gene_ensembl")
tx = transcriptsBy(yeastDb)

Here again, tx provides some strand info. If I now want to extract the per base
coverage of a transcript that lies on the - strand.
How do I do that? I have the coordinates of the transcript via coord(tx). But
how do I assure that get the correct info?

I hope I have made myself clear and I would really appreciate any comments.

Probably is working fine out of the box, I just want to make sure that I dont
make a mistake in the very first steps.

Best,
tefina