Question: Unable to view aligned reads in IGB after loading BAM file
0
gravatar for aravin.sukumar
4 weeks ago by
aravin.sukumar0 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 • 76 views
ADD COMMENTlink modified 4 weeks ago by Jennifer Hillman Jackson23k • written 4 weeks ago by aravin.sukumar0
0
gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 4 weeks ago by Jennifer Hillman Jackson23k
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