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igvteam / igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
MIT License
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igv-reports doesn't display bam but igv does #57

Closed azbard closed 2 years ago

azbard commented 2 years ago

Absolute noob here - be gentle.

Is there any conceptual reason why a bam/bed combo would display fine in igv proper (java) but only the bed shows up in a report generated as follows?

create_report bedfile.bed hg19.fasta --tracks bamfile.bam

These two made with the same files... Screenshot 2021-12-14 151244 image

[edited to show matching locations in igv and igv-reports]

jrobinso commented 2 years ago

In your igv-reports screenshot I see chr20 is displayed, but in the IGV desktop screenshot chr5. If you are displaying the chr5 data at the chr20 location then you won't see any alignments. I think this is the root cause, but its difficult to say how this could occur without having the files. If you're able to share the report (generated html) you can email it privately to igvteam (at) broadinstitute.org and I will have a look.

jrobinso commented 2 years ago

Thanks for the data. I think your bed file might be malformed, based on the table column names in your screenshot above. Could you zip and attach it (just the bedfile).

jrobinso commented 2 years ago

Actually the table column names is a report bug, it would still be useful to see the bed file. You can zip and attach it here, or email to the igvteam email you sent the report to.

azbard commented 2 years ago

I figured out the report not showing the tracks - my pysam library was causing the problem - it had been altered for another project. Ugh - this was all my own fault.

The bed though... bedfile-copy.zip

jrobinso commented 2 years ago

OK, python is like that. RE the bed file, "bed" uses zero-based coordinates, unlike other formats like VCF and GFF. So your start coordinate should be 1 less than the end coordinate for 1-base variants.

On Wed, Dec 15, 2021 at 5:52 AM Adam Z Bard @.***> wrote:

I figure out the report not showing the tracks - my pysam library was causing the problem - it had been altered for another project. Ugh - this was all my own fault.

The bed though... bedfile-copy.zip https://github.com/igvteam/igv-reports/files/7719868/bedfile-copy.zip

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ankit-21 commented 2 years ago

Thank you for your support and prompt response to our issue. We were able to get igv-reports to function as desired. Really love this tool. Feel free to close this issue.