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Question: Unable to view aligned reads in IGB after loading BAM file
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gravatar for aravin.sukumar
12 months ago by
aravin.sukumar • 0
aravin.sukumar • 0 wrote:

Hello everyone,

I downloaded an SRA file from a GEO accession and converted it to a BAM file using sam-dump. I tried to view the BAM file using IGB and IGV but the aligned reads to not show up on the viewer. For IGB, I clicked load data but the sam-dump track is empty. I used the linked to IGB from the Galaxy site. Should I try downloading the BAM file first or is there another issue?
rna-seq igb bam • 485 views
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modified 12 months ago by Jennifer Hillman Jackson ♦ 25k • written 12 months ago by aravin.sukumar • 0
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gravatar for Jennifer Hillman Jackson
12 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The dataset only includes the reads in BAM format. There are no alignments. Convert to SAM format if you want to inspect and verify this yourself.

For most use cases in Galaxy, downloading the fastq data is best, since most tools do not accept sequence data in BAM format. This includes the mapping tools available at https://usegalaxy.org.

Sometimes data sourced from NCBI SRA needs to be reformatted. This is not the case with the accession you are using, but it may come up in the future. How-to: https://galaxyproject.org/support/ncbi-sra-fastq/

Support FAQs: https://galaxyproject.org/support/

Galaxy tutorials: https://galaxyproject.org/learn/

Hope that helps! Jen, Galaxy team
ADD COMMENT • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k
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