Adding bam file (Any file) as URL

Question

[rse]

Hello,

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

Thanks in advance.

Regards Raman

[steve]

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

[rse]

Thanks. I have tried IGV :)

[finswimmer]

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

[rse]

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

[Pierre Lindenbaum]

• Bam file view in ucsc
• How to visualize a bam file in UCSC Genome Browser
• Converting Bam To Bedgraph For Viewing On Ucsc?
• How to upload my own BAM file to UCSC genome browsers?
• ....

Answer 1

[Emily]

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

[rse]

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

[Emily]

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.

[rse]

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

[Devon Ryan]

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.

[rse]

Sure, i will try it out. Thanks :)