UGENE Forum - Insertions in NGS alignments

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UGENE Forum › General Category › Feature Requests › Insertions in NGS alignments

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Insertions in NGS alignments (Read 7175 times)

May 24^th, 2019 at 8:10am

JP Offline
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Dear developers, thank you for this incredibly useful, and free, software. Are you planning to add insertion visualizations when viewing bam files in a manner similar to IGV ("I" and sequence in a floating window)? This is a very important piece of info when analyzing CRISPR experiments. Currently, only deletions are shown, which can be somewhat misleading. Thanks!

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Reply #1 - May 24^th, 2019 at 1:44pm

Olga Golosova Offline
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Posts: 338

Quote:

Dear developers, thank you for this incredibly useful, and free, software.

Thank you for the feedback!

Quote:

Are you planning to add insertion visualizations when viewing bam files in a manner similar to IGV ("I" and sequence in a floating window)?

Right now we do not have some particular plans on that, but thank you very much for the idea! We'll keep this in mind when planning the future UGENE versions.

Quote:

Currently, only deletions are shown, which can be somewhat misleading.

Of course this will not replace the necessity of the feature you've proposed, but you might pay attention on the cigar information shown for each particular reads in its hint. See this link: https://ugene.net/wiki/display/UUOUM32/Getting+Information+About+Read.

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Reply #2 - May 24^th, 2019 at 6:24pm

JP Offline
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Agreed, and samtools view | cut will be even easier. However, coupling the convinience of UGENE with indel quantification software such as Pinello Lab CRISPResso will be a marriage made in heaven for everybody in genome editing studies.

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Reply #3 - May 27^th, 2019 at 1:34pm

Olga Golosova Offline
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Posts: 338

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coupling the convinience of UGENE with indel quantification software such as Pinello Lab CRISPResso will be a marriage made in heaven for everybody in genome editing studies

))))
Yes, this would be nice.

However, this is not just a minor improvement, it's better to do such work in terms of some big project (grant, etc.).

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