Question: Conversion of SAM to BAM file
gravatar for dikshagarg0409
19 months ago by
dikshagarg04090 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
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson25k • written 19 months ago by dikshagarg04090
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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

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

Thanks! Jen, Galaxy team

ADD COMMENTlink written 19 months ago by Jennifer Hillman Jackson25k
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