Hello Synapse Developers,
I am wondering if it would be possible to request the raw .fastq files that were used for the [syn4896408](https://www.synapse.org/#!Synapse:syn4896408) epigenetics study prior to the pooled control and individual ROSMAP samples being sorted and mapped to the GRCh37/hg19 genome? I would like to align them to a more updated version of the human genome (i.e. GRCh38/hg38) using alternative mapping tools currently available. If this is anyway possible (?), then please let me know and we can follow up with next steps for access.
Thank you so much,
Phoebe
Created by Phoebe Valdes prvaldes Hello,
I do not see raw fastq files on Synapse for this study, so I think there are two options:
1. They do provide the BAM files (syn5958425), which might be convertible to un-aligned fastq via samtools ([examples here](https://www.metagenomics.wiki/tools/samtools/converting-bam-to-fastq))
2. You could try contacting the corresponding author, Phil De Jager (pld2115@cumc.columbia.edu), and see if they still have the original fastq files.
I hope one of those options works for you. Let me know if you have any other questions.
Jaclyn
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