I?m using the bulk RNA-Seq dataset from syn21589959. I set up the pipeline for bulk RNA-seq and I tried to compare it with the preprocessed data set (ROSMAP_RNAseq_FPKM_gene.tsv ; syn3505720). But I think the expression table doesn?t match the fastq files. I tried to match the data using ?ROSMAP_assay_rnaSeq_metadata.csv?, ?ROSMAP_biospecimen_metadata.csv?, ?ROSMAP_clinical.csv?, and ?ROSMAP_IDkey.csv? The fastq files have a name like this (RISK_100_S63_R1_001.fastq.gz, syn21589959). But the expression table has the other name(column), and I only can find a bam file. These bam files are generated after mapping? Can I get the fastq files corresponding to the expression table? ([syn3505720](https://www.synapse.org/#!Synapse:syn3505720)ROSMAP_RNAseq_FPKM_gene.tsv). I need the raw sequencing data for processing. I really look forward to getting your reply. Thank you.

Created by Tamina Park tamina
Thank you very much @lheath That's what I wanted to know. I'm sure it'll help. Sincerely, Tamina
Hi @tamina, I did some searching and found the fastq files that correspond to the expression table you are interested in. They are in a different folder, as this effort was part of a larger project across cohorts (that is not intuitive--even I had to ask where to find them). The fastq files with specimenIDs that match the expression table are in [syn8612097](https://www.synapse.org/#!Synapse:syn8612097). If you look around in this set of folders in synapse, you may find more fastq files from other cohorts to experiment with as well, and also downstream differential expression analyses . I hope this helps! Best, Laura

Where can I find the raw fastq files corresponding to the expression table (syn3505720)? page is loading…