Dear community,
I have a very little quick question: I have directional paired-end RNAseq data which I want to put in the UCSC genome browser in a form which the same track displays as positive values forward reads and negative values reverse reads. Do you know a way to do it?
Below I paste an image found on google to show an example of what I want to do:
Thanks for your help!!!!!
•
written
by
daniel.soronellas
Unstarch the results into bedgraph format, applying a negative score to the reverse-strand result set:
$ unstarch forwardStrandBins.starch \
| awk '{ \
print $1"\t"$2"\t"$3"\t"$5; \
} \
}' - \
> forwardStrandBins.bedgraph
$ unstarch reverseStrandBins.starch \
| awk '{ \
print $1"\t"$2"\t"$3"\t"(0-$5); \
} \
}' - \
> reverseStrandBins.bedgraph
Merge the bedgraph files:
$ sort-bed *.bedgraph > final.bedgraph
Add any desired metadata and display parameters to final.bedgraph.
final.bedgraph as a custom track in your UCSC Browser instance.Once you have the process down, some of the above steps can be condensed to handle forward- and reverse-stranded data with one step.
you assumed that forward and reverse reads do not overlap, which may not be true.
Good point — will try to come back to this answer with an update at some point.
You can just generate + strand and - strand bigWig files separately,negate the minus track, and then build a Collection of the ones you want to do overlay following this tutorial . The only difference from the tutorial you have to make is to choose "transparent" as the merge method instead of "add"
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