Manual curation of annotated genes?

Question

[DanielC]

Dear Friends,

I have got an assembled contig of a bacteriophage. I have the annotation file from prokka and now I want to manually curate the annotation by visualizing the annotation features on the contig aligned with top 20 blast hits of the contig. Can anyone please let me know how can I do that? I tried tablet, but I don't think they have the feature to align more than one fasta file.

Right now with tablet, I can open SAM file of the reads mapped onto the contig and the reference contig fasta file. What I am looking for is to also align the 20 blast hits to the contig and then visualize the annotation. In general, a tool to manually curate the annotation.

Thanks,

Answer 1

[Michael]

Then you need some tool to convert blast results into a format that tablet or IGV can understand, maybe GFF in IGV, so that's a script that one would call Blast2Gff.pl here or have a look at this post How To Convert Blast Results To Gff

Finally, open all your files in IGV and there you go.

[DanielC]

Thank you for this! I would really appreciate your input on the data generated after this:

So, now I have the:

--> annotated gff file from prokka of the assembled contig

--> gff file of the 20 best blast hits (of the assembled contig) The GFF file looks like this:

KC139526.1      BLASTN  hsp     13946   15668   0.0     -       0       Match CBphage_assembly-spades-25000-readsae:NODE_1_length_88156_cov_48.969578
KC139526.1      BLASTN  hsp     34229   36058   0.0     -       0       Match CBphage_assembly-spades-25000-readsae:NODE_1_length_88156_cov_48.969578
KC139526.1      BLASTN  hsp     36062   37169   0.0     -       0       Match CBphage_assembly-spades-25000-readsae:NODE_1_length_88156_cov_48.969578
KC139526.1      BLASTN  hsp     13190   13696   0.0     -       0       Match CBphage_assembly-spades-25000-readsae:NODE_1_length_88156_cov_48.969578
KC139526.1      BLASTN  hsp     37315   37446   7e-50   -       0       Match CBphage_assembly-spades-25000-readsae:NODE_1_length_88156_cov_48.969578

--> assembled contig fasta file

--> SAM file of the reads mapped onto the assembled contig

--> protein domain hits from interproscan for the annotated genes (for functional annotation) in GFF format

Could you please let me know on how to visualize all this data at once in IGV; I have not used IGV before, would really appreciate your input.

Thanks much!

[DanielC]

asked as a new question: "Manually curate gene annotation by visualizing on IGV or tablet or any better visualization tool"

Please let me know of your comments. Thanks!