Question: Unable to view aligned reads in IGB after loading BAM file
0
gravatar for aravin.sukumar
9 months 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 • 325 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by aravin.sukumar0
0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k 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 9 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 84 users visited in the last hour