Question: Visualize location of genes on Chromosomes
1
gravatar for kevluv93
3.4 years ago by
kevluv93150
United States
kevluv93150 wrote:

I'm trying to create a figure which visualizes the locations of NBS-LRR genes on chromosome 1 on the watermelon genome based on the watermelon sequencing genome paper here. Essentially, I want to create a chromosome map of locations of specified genes for a figure.

I've tried to set up the watermelon genome as a database for BLAST, and while it did give me the numeric location of these genes on the watermelon genome, it doesn't do a good job with "visualizing" where the genes lie on the chromosome.

I'm thinking about using bowtie to align these sequences to chromosome 1 and then visualizing their locations and alignment in IGV. But can bowtie be used for aligning single "reads" of a very large size to a chromosome?

Can anyone suggest a program or tool to create a chromosome map of specified genes given the target genome and DNA sequences of interest? Thank you!

blast rna-seq alignment genome • 1.8k views
ADD COMMENTlink modified 3.4 years ago by Alex Reynolds28k • written 3.4 years ago by kevluv93150

You wouldn't need a bowtie alignment if you already have the genome coordinates from BLAST. Can you not just upload the genome coordinates of the genes you're interested in?

ADD REPLYlink written 3.4 years ago by jotan1.2k
0
gravatar for Jean-Karim Heriche
3.4 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

Have a look at genoverse (code on GitHub).

ADD COMMENTlink written 3.4 years ago by Jean-Karim Heriche18k
0
gravatar for h.mon
3.4 years ago by
h.mon24k
Brazil
h.mon24k wrote:

You can do what you want with both Spaln and GMAP. Both output GFF3 and SAM, so the results are easily viewed on IGV. Bowtie is not a good fit for this task indeed.

ADD COMMENTlink written 3.4 years ago by h.mon24k
0
gravatar for Alex Reynolds
3.4 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

If you're making a web figure, this AngularJS directive might be useful.

ADD COMMENTlink written 3.4 years ago by Alex Reynolds28k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1134 users visited in the last hour