Oliver (and interested others)
I've now added BAM files made from mapping my paired end data as if it were single end data to GBrowse. A useful example can be seen here. The bottom track shows the paired end mapping BAM file and the two tracks above are the F and R reads mapped as single end data. In all cases forward strand alignments are coloured green and reverse strand alignments in the salmony-orange colour.
Some things to notice are that in the paired end mapping track, the reverse reads shows the reverse strand base and not the forward strand one (which is what seems to be the standard). There are also a mix of + and - strand alignment in the F and R tracks, which I didn't expect (maybe I'm missing something obvious though?).
This actually highlights an interesting point: If the - strand alignments shows the + strand base, it will be impossible to see C bases that were converted by the bisulfite treatment unless there is a way to specifically colour either the methylated bases or the bases that were converted (more interesting would be the methylated bases). As for the paired-end BAM files, even in the single end files C bases that were converted still aren't shown as miss matches. I need to learn about the SAM file format to understand why this is - so far I've been rather blindly making things work rather than getting into the proper details.
I've now added BAM files made from mapping my paired end data as if it were single end data to GBrowse. A useful example can be seen here. The bottom track shows the paired end mapping BAM file and the two tracks above are the F and R reads mapped as single end data. In all cases forward strand alignments are coloured green and reverse strand alignments in the salmony-orange colour.
Some things to notice are that in the paired end mapping track, the reverse reads shows the reverse strand base and not the forward strand one (which is what seems to be the standard). There are also a mix of + and - strand alignment in the F and R tracks, which I didn't expect (maybe I'm missing something obvious though?).
This actually highlights an interesting point: If the - strand alignments shows the + strand base, it will be impossible to see C bases that were converted by the bisulfite treatment unless there is a way to specifically colour either the methylated bases or the bases that were converted (more interesting would be the methylated bases). As for the paired-end BAM files, even in the single end files C bases that were converted still aren't shown as miss matches. I need to learn about the SAM file format to understand why this is - so far I've been rather blindly making things work rather than getting into the proper details.
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