Hi !!!
I was curious to check how to request the raw fastq files from AMP-PD. Based on tier2 access one can get access to the genomics file. The Tier2 access link leads me to the results of the transcriptomics analysis. However these bucket does not enlist the path to the fastq files on which various pipelines were executed. Is there a Tier 3 access perhaps to request the raw fastq sequencing files?
Thanks for your help.
Cheers,
Shaun!
@hirotaka would you happen to have insight maybe??
Hi @bshaun and @ecebayram , personally I’ve never used fasq by myself, so I am sorry that I cannot help. Have you contacted the support? Their support team is very responsive and helpful!
I did contact the admin at admin@amp-pd.org sometime back.
I think the fastq shares a different storage bucket from the analysis files. I will wait for their response. Not a problem! Thanks!
I believe they are on a different storage tier to save money but I’d have to check.
The BAM files include unmapped reads so a BAM → fastq is also an option depending on what you want to accomplish. Those are in the amp-pd-transcriptomics bucket under samples/rnaseq/star.
Yes @ehutchins - Thanks for your response. I am processing the samples like you suggested. I converting them back to fastq from bam as of now until I hear back from amp-pd admin.
Okay glad that is working out. Happy to chat if you need anything. 
Transcriptomics is my jam and I was a member of the transcriptomics working group for AMP PD.
Thanks so much @ehutchins Elizabeth! I would follow up with you and would love to chat. Yeah AMP PD transcriptomics was a huge effort and needless to say all the work you all did in that woking group is really so extraordinary and so helpful!
Oh there was a huge team and great work by all and I was one small part of that. Sounds great, let me know!