I have been playing for the first time with deeptools lately by ploting some metagene and I have a question I don't manage to get around.
As suggested in another post I extracted forward and reverse strand mapped reads on separated bedgraph tracks from the bam file with bamCoverage.
In the below command line example I focus only on forward gene. I performed an overlapping join between the forward gene start/end and both reverse and forward mapped reads. This step led me to keep matching forward strand bedgraph regions as the trans signal and the reverse ones as the cis signal. I finally exported cis and trans signals as separated bedgraph to be converted into bigwig tracks.
However I am not sure of the results I got after plotting both cis and trans signal according to forward gene positions. Cis signal should have the right orientation but I guess the trans signal start and stop should be switched according to transcription direction ? In the same spirit, working with minus strand gene region would switch the cis signal which is ok, but it would also switch the trans signal which is an issue.
Could you confirm that deeptools can't handle this case ? Or am I misinterpreting something ?
Any help will be appreciated !
The command line
computeMatrix reference-point --referencePoint TSS -S bigwig/cis.forwardgenes.bw bigwig/trans.forwardgenes.bw -R gtf/forwardgenes.bed -b 1000 -a 1000 --skipZeros -o computeMatrix/Cis_trans.centered.TSS.forwardgenes.gz &> output.plus.genes.txt
plotProfile -m computeMatrix/Cis_trans.centered.TSS.forwardgenes.gz \
-out plot/Cis_trans.centered.TSS.forwardgenes.png \
--perGroup \
--plotTitle "Forward genes cis and trans signal centered on TSS"
Hi guys!
I have been playing for the first time with deeptools lately by ploting some metagene and I have a question I don't manage to get around.
As suggested in another post I extracted forward and reverse strand mapped reads on separated bedgraph tracks from the bam file with bamCoverage.
In the below command line example I focus only on forward gene. I performed an overlapping join between the forward gene start/end and both reverse and forward mapped reads. This step led me to keep matching forward strand bedgraph regions as the trans signal and the reverse ones as the cis signal. I finally exported cis and trans signals as separated bedgraph to be converted into bigwig tracks.
However I am not sure of the results I got after plotting both cis and trans signal according to forward gene positions. Cis signal should have the right orientation but I guess the trans signal start and stop should be switched according to transcription direction ? In the same spirit, working with minus strand gene region would switch the cis signal which is ok, but it would also switch the trans signal which is an issue.
Could you confirm that deeptools can't handle this case ? Or am I misinterpreting something ?
Any help will be appreciated !
The command line