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Question: Freeing up memory space/Converting BAM files
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gravatar for joseph.andrews
14 months ago by
joseph.andrews • 20
Canada
joseph.andrews • 20 wrote:

Hello

I have deleted and purged permanently all histories and data, and yet I am told I am using 97% of my available space. logging out and back in does not affect this calculation. Can you advise, as I have a new project I am working on? Secondly, Is there a tool for converting BAM files created using human build HG19 to HG18?

Thanks in advance

Joe
convert account perm-delete coordinate quota • 322 views
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modified 14 months ago by Jennifer Hillman Jackson ♦ 25k • written 14 months ago by joseph.andrews • 20
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gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For the account quota, your situation is the same as in this post (deleted but not permanently deleted data is present) and the same solution will apply: https://biostar.usegalaxy.org/p/24830/

For the conversion, BAM datasets cannot be mapped to another genome build directly with the tool Lift-Over > Convert genome coordinates between assemblies and genomes. The input must be in BED, Interval (but formatted the same as strict BED), or GTF format. The alternative is to remap the fastq data against hg18.

Convert BAM to BED with the tool BEDTools > BAM to BED converter or NGS: BamTools > Convert, Merge, Randomize.

Tips:

Thanks! Jen, Galaxy team
ADD COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
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