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Question: How to visualize bam, bed and vcf files programmatically using Python and Shell or a Linux software?
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How to visualize bam, bed, and vcf files programmatically using Python and Shell or a Linux software? Have these files coming from the NGS microbial data processing pipeline, need to make charts and plots from them, looking for a proper robust software packages for Linux OS.

ADD COMMENTlink 10 months ago informatics_warwick • 0 • updated 10 months ago dariober 10k
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What you mean by "visualize programmatically"?, however, to visualize bam or bed files you can use IGV, you can visualize more than one file at the same time (if you mean that).

ADD REPLYlink 10 months ago
Buffo
♦ 1.6k
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For anyone using Windows, EaSeq has some nice functionality to do this with different sorts of visualizations outside of just tracks. Unfortunately, it's a Windows only program.

ADD REPLYlink 10 months ago
jared.andrews07
♦ 2.4k
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Hello informatics_warwick!

We believe that this post does not fit the main topic of this site.

Not a real question

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink 10 months ago
Michael Dondrup
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RSeQCoffers a variety of graphics for alignment QC. Some of the tabular output files can afterwards be nicely visualised using multiQC.

ADD COMMENTlink 10 months ago michael.ante ♦ 3.3k
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Assuming that by "visualize" you mean showing coverage and/or alignments in genomic windows, you can use Gviz if you are ok with R. For quick, explorative visualization directly from the command line I wrote ASCIIGenome.

ADD COMMENTlink 10 months ago dariober 10k
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