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 usegalaxy.org 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?
- 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 :)