Hi all, I am working on a GRO-Seq data and I want to plot a graph like one these figures, plus and minus strands are reversely merged on the same line. I know that UCSC genome browser can handle this, but in many ways, it becomes user-UNfriendly. So does anyone know a tool or GUI which can plot a graph like this?
1 answer
For the ones who have suffered from the same problem;
Apparently, GRO-Seq figure is independent of the tool. It is possible to get a visualization as in the link above with any browser. I used Homer for GRO-Seq analysis. The trick is, when it comes to generating the bedgraph using makeUCSCfile command, first separate +/- strands using makeUCSCfile tagDirectory/ -strand + -o plus_strand.bedGraph and for - strand, makeUCSCfile tagDirectory/ -strand - -neg -o minus_strand.bedGraph. the command with -neg will give you a bedGraph with (-) values. before merging them, you may need to remove the trackline information since it may cause an error when sorted. then with using a simple cat command, merge the two, then sort them using sort -k1,1 -k2,2n fileName.bedGraph. then gzip your bedGraph. Now you can even put it to IGV and it will give +/- strands in the same line.
Log in to answer this question.
-
Alternatives to Lollipop for virus variant data
written by ch504 •
-
FANTOM5 enhancers: intepretations
written by c.clarido
-
ChIPseq vs RNAseq results comparison
written by V
-
BigWig file of strand-specific RNA-seq data
written by yuabrahamliu •
-
How to Get Nucleotide/Allele Frequency Spectrum From NGS SAM/VCF File
written by liaoyunshi •
-
Heatmap for RNA-Seq data
written by chetana •
-
Plotting copy number varation: amplification and deletion data from GISTIC
written by missnc •
-
Extracting intergenic region coordinates and type
written by timjoncooper
-
Creating neo4j graph databases from UCSC tables browser
written by John
-
Lab Web Framework, Any Suggestions?
written by daniel.soronellas
