RNA-Seq based prediction

Discussions about predicting genes with AUGUSTUS. Not covered here: WebAUGUSTUS and BRAKER1

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katharina
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Re: RNA-Seq based prediction

Post by katharina »

by Mbandi on 30.10.2014 - 14:47
hints from multiple BAM files
Hi,
I was wondering if it makes sense to generate hints separately from multiple BAM files and merge the hints. Does read coverage play a role in generating hints? If this is the case, then reads that support one intron junction could be located in separate file. Would it then not be appropriate to merge BAM files prior to generating hints?
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Re: RNA-Seq based prediction

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by katharina on 30.10.2014 - 16:34
If possible, BAM files should be merged prior generating hints.
If this is not possible (due to size and number of libraries), the intron hints from separate libraries can easily be joined (e.g. use Perl). For the exonpart hints, it is more complicated. One approach that we have not tested, but seems rather easy is the usage of wiggletools (https://github.com/Ensembl/WiggleTools) to add coverage of several libraries prior hint conversion.
Another approach is to join only those bam files that biologically belong "together", i.e. from the same biological condition. This may make sense if you assume alternative transcript expression under different conditions.
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Re: RNA-Seq based prediction

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by Mbandi on 03.11.2014 - 14:42
Hi Katharina,
After generating my BAM files, I have notice that the '--paired' flag suggest that paired reads are on opposite strands of same target. If you use tophat, you have access to the following orientations:
fr-unstranded, fr-firststrand and fr-secondstrand. Is the paired option only applicable for unstranded libraries?
Thanks
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