Fastq and Bam file mapping to sample IDs in Berg Patchseq transcriptomic dataset

Technical
, , ,
1

Hello, we were recently approved for access to the Berg patch-seq transcriptomic data and wanted to do some preliminary analyses with the initial raw fastq files. I wanted to ask if there is a resource that would allow us to map the (pairs of) fastq files and bam files to sample IDs in the processed count matrices?

For instance, I am not sure what sample ID corresponds to “BT170919-01_E1-50_ACTCGCTA-ACTGCATA.fastq.tar” (nor am I 100% sure what its strand-complement file is) or “ar_656576285_STAR_Aligned.sortedByCoord.out.bam.tar”. I would guess that the fastq file in my example corresponds to one of the samples starting with “BT170919-01_E1-50_”, but I am not sure which.

I have looked for “ACTCGCTA-ACTGCATA” and “656576285” in the metadata and file manifests downloaded from Multimodal Characterization of Individual Neurons - brain-map.org and was not able to find either in any of the spreadsheets provided. There were not any other supplementary data through our download via NeMo/Aspera.

Thank you very much for any tips/help!

2

For others having the same issue, this has been solved. We cannot share identifying information publicly, but please post in this thread and we can reach out directly to share the conversion table. If you would like access to the human patch-seq data, please follow the instructions for requesting access via the NeMO Archive. The relevant data set is “lein_pseq_tx”.