Plotting bar graph with contigs from assembly in zebrafish chromosome?
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5.8 years ago
Amk ▴ 120

Dear All,

I am new to genomics. Kindly forgive if this question doesn't make sense. 
I have thousands of contigs from an assembly. I came across a paper where they have plotted a bar graph of the assembled contigs of Carp fish species across the chromosome of Zebrafish (Find it here). I am confused of extracting the data to plot graph like that. Is there any way to compare my contigs with the transcriptome data and plot like that. I came across much difficulty in text based comparison of the genes as it have errors. If you have any strategy in your mind please feel free to share. Thank you.


Regards,
AMK

Transcriptome Graph Chromosome • 1.2k views
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5.8 years ago
Chris Cole ▴ 760

If you mean Figure 3 in the paper then this bit in the methodology applies: "All collected contigs were BLASTed against zebrafish protein database for identifying coding strand and orientation".

Simply BLAST the contigs against the reference to determine their chromosomal positions. Then, collate the information of which chromosome has the best match for each contig and plot it.

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Dear Chris,

Thank you for the suggestion. This gave me an idea.

Regards,
Amk

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