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Question: Conversion of SAM to BAM file
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gravatar for dikshagarg0409
19 months ago by
dikshagarg0409 • 0
dikshagarg0409 • 0 wrote:

SAM file is converted into BAM file but problem is that it cannot be open in galaxy. How it will be open could you help me out from this problem. I shall be very thankful to you.

bwa • 574 views
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modified 19 months ago by Jennifer Hillman Jackson ♦ 25k • written 19 months ago by dikshagarg0409 • 0
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gravatar for Jennifer Hillman Jackson
19 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

BAM datasets are a binary compressed version of SAM datasets. These cannot be opened and viewed directly. To view the contents in plain text, use the SAM file. Other tools in the Samtools and Picard tool groups offer methods to filter and summarize the data.

If you instead want to visualize the mapping results of a BAM dataset against a reference transcriptome/genome, there are a few choices depending on the assigned database.

Any genome/transcriptome:

  • Trackster: This tool is built into Galaxy, found under "Visualizations" or the small graph icon within the expanded dataset. If you are using a Custom reference genome, it needs to be promoted to a Custom build and then that database attribute assigned to the datasets to visualize.

Many common genomes:

If the database is assigned, one or more of these links will be available within the expanded dataset for the viewers that are indexed for the same reference genome as assigned as the "database" of the dataset(s) to view.

  • UCSC main
  • IGV (local or public)
  • IGB
  • bam.iobio.io

How to format a Custom genome/transcriptome and promote it to a Custom Build:

Thanks! Jen, Galaxy team
ADD COMMENT • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k
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