Question: 100 GB bam dataset fails conversion to bam.bai
gravatar for supinder84
14 months ago by
supinder8410 wrote:

Hi! I'm a beginner to RNA-Seq world and need assistance to correctly analyze our dataset.

I'm working on approximately 100 GB RNA-Seq raw data (.bam files). I'm analyzing this data on usegalaxy to compare differential transcriptome expression under two conditions. My account, which provides 250 GB free space, does not complete the assigned tasks as it runs out of space in the middle of the assigned task for conversion of .bam file to FASTQ -the very first step in the analyses workflow. It would be great if you can help me- 1. To calculate the approximate space I would need in usegalaxy server/cloud and the corresponding price. 2. How to process request for more space in usegalaxy and the contact of concerned person?

  1. Kindly share your opinion on RNA-Seq workflow I'm following to analyze differential transcriptome expression under two conditions using mouse cells. I have received .bam files from the sequencing service providers. WorkFlow: a) .bam to FastQ conversion; b) FastQC for all the samples; c) FastQ groomer if needed; d) Alignment using mm10/GRcm38 mouse genome by Tophat tool (gives .bam files); e) HTseq for counting the expressing transcripts; f) cuffdiff for DGE, cuffmerge to pool the data replicates; and g) DAVID or g:profiler to categorize gene ontology and related pathways.

Awaiting your response, Supinder :)

convert bam.bai bam dataset • 396 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by supinder8410
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The job likely ran out of memory during execution. BAM datasets over 25-45 GB (content matters) approach the maximum size for data conversions/upload.

A job running out of memory (failing, red dataset) - if that is what is occurring - is unrelated to account disc space. Rather, the job is either tool large to execute at Galaxy main or there is possible a usage problem.

I suggest uploading the data in fastq format instead of BAM. If that data remains still too large (exceeds the account quota), and you are working for an academic research project, we may be able to offer more account disc space. Send us an email to from your registered account email at, include a link to this post, a short description of your project, and we can review.


Learn (protocols):

Support (includes troubleshooting):

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 14 months ago • written 14 months ago by Jennifer Hillman Jackson25k
gravatar for supinder84
14 months ago by
supinder8410 wrote:

Thanks, Jen. I will try to analyze my data again as suggested in your response and will get back to you.

I hope it works this time! Supinder

ADD COMMENTlink written 14 months ago by supinder8410
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