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Adding bam file (Any file) as URL

Hello,

How should i add my data (for eg. a BAM file) as URL (either http, https or ftp)?

Thanks in advance.

Regards Raman

next-gen sequencing
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updated by steve steve • written by rse rse

Hello rse ,

your post is missing essential information about what you are trying to do and why. Please elaborate more on it, so someone can help you .

fin swimmer

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written by finswimmer finswimmer

Hello fin swimmer,

I want to view my data in public browsers (UCSC, Ensembl). So i want to add my data to a public url.

Regards

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written by rse rse

Based on this statment

i have a 200 GB file to upload

I am going to recommend trying IGV on your local system first

http://software.broadinstitute.org/software/igv/

It can be run on your desktop, and also headlessly from your Linux server via X11 window + ssh

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written by steve steve

Thanks. I have tried IGV :)

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written by rse rse

1 answer

You can host the data on CyVerse which will then allow you to attach your files to view in genome browsers.

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written by Emily Emily

Thanks Emily. I tried using CyVerse, but the maximum upload size limit per file is 1.9 GB and i have a 200 GB file to upload

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written by rse rse

You're not going to find anywhere to host that size of data for free. Check with your Institute IT systems what options they have.

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written by Emily Emily

Sure, thanks :) I will probably extract that regions from bam file and make smaller bam files

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written by rse rse

You might get lucky and be able to use usegalaxy.org or usegalaxy.eu (don't know what their quotas are). Galaxy will create temporary links for UCSC and similar sites. Realistically, you'll want to make a bigWig so you can navigate your coverage data in a reasonable amount of time. That will also be vastly smaller.

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written by Devon Ryan Devon Ryan

Sure, i will try it out. Thanks :)

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written by rse rse

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