Visualize genome and blast hits

Question

[krzysieksobieszek]

Hi! I have a few sets of multiple fasta files (mostly genes and huge set of markers) in .fasta formatted with only name tags (no separated description or something) and genome sequence in multiple fasta .fa file (it's formatted similarly as previous as 21 superscaffolds/chromosomes). I also have BLAST files for all the sets against genome in few formats (also tabular/CSV). So I have this genome and all the sequences with corresponding hits, but I'm struggling how to map them on the genome(visualy display as map which will correspond to sequences lenghts). I was already trying few programs but I'm challenging some problems with data size or format. I think there need to be something which can display that data and I was thinking on using R but I'm a newbie and I don't really know how. I'm hoping for your help and suggestion.

[Pierre Lindenbaum]

circos http://circos.ca/

[ggman]

you could try IGV http://software.broadinstitute.org/software/igv/

[WouterDeCoster]

I changed your title to make it more specific, I hope it's still accurate.

I'm not sure what exactly you are looking for, but what about this: karyoploteR: uncircle your genomes

[krzysieksobieszek]

karyoploteR looks nice and accurate. It might be hell giving it all the arguments but it's looking like it might get the job done. The problem is I can't install it on my machine. I have R 3.4 and Bioconductor 3.5. I was allready trying on installing packages by hand and updating Bioconductor in R but I'm still getting the same warnings listed below:

Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘openssl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘curl’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘httr’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biomaRt’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationHub’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
10: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
11: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationFilter’ had non-zero exit status
12: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Rsamtools’ had non-zero exit status
13: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicAlignments’ had non-zero exit status
14: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
15: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BSgenome’ had non-zero exit status
16: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
17: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘VariantAnnotation’ had non-zero exit status
18: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘ensembldb’ had non-zero exit status
19: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘regioneR’ had non-zero exit status
20: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biovizBase’ had non-zero exit status
21: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘karyoploteR’ had non-zero exit status

Do you happen to know what am I doing wrong?

[WouterDeCoster]

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[WouterDeCoster]

The cause is the openssl package, at the root of the dependency tree. Googling installation of package ‘openssl’ had non-zero exit status will tell you which system package you need to install, depending on your operating system. e.g. sudo apt-get install libssl-dev for Ubuntu...

[krzysieksobieszek]

I have already tried circos before and it's not exactly doing the job (or maybe it is but I have definitely too many sequences to make it in one table showing all the dependencies). I forgotten about IGV but it's also not very suitable since it's mostly oriented on expression data which I don't have. I would try karyoploteR for now since it's looking most promising. Thanks guys for such fast reply. What I want to obtain is something more like genetic map but incorporating physical position data. Something looking like this: http://www.yourgenome.org/sites/default/files/illustrations/diagram/genetic_mapping_linkage_drosophila_yourgenome.png

[WouterDeCoster]

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Answer 1

[Joe]

You could try BRIG, as it literally displays blast hits against a reference sequence, somewhat like circos.

If you're happy working in Python too, I quite like BioGraPy http://apierleoni.github.io/BioGraPy/

It's still in development though so may not entirely do what you need.

[krzysieksobieszek]

Unfortunately BRIG doesn't work with my data (it's too big) and I also have some issues with making BioGraPy working. First there was the installation issues on declare.namespace part and with directories during installation but just when I thought I have overcome them and try to run some test code it just collapsed as follows:

File "/home/krzysiek/Desktop/apierleoni-BioGraPy-9418682/MOJAproba.py", line 1, in <module>
    from biograpy import Panel, tracks, features
  File "/usr/local/lib/python2.7/dist-packages/biograpy-1.0a0dev_r0-py2.7.egg/biograpy/__init__.py", line 1, in <module>
    declare_namespace(__name__)
NameError: name 'declare_namespace' is not defined

Do you have any further suggestions or idea what to do to make BioGraPy working (I found it rly straightforward so it might fit my data)?

[WouterDeCoster]

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[Joe]

If BRIG is no good, a similar but newer tool is ANVIO, though I still wouldn't exactly call it beginner-friendly. I can't offer you much help with BioGrapy, as it's experimental, and I've not used it extensively. I was able to install it without issues before (suggest you try installing it in an Anaconda/miniconda environment).