Hello, I am interested in looking at the umapped fq files and it seems the format across the files is not standard nor as indicated in the annotation. For example, syn4055334 is not a fastq file while syn5519739 is a fastq file? When I attempt to convert syn4055334 from sam to bam via: samtools view -bS BM_10_652.unmapped.fq > unmapped_BM_10_652.bam I get both a parse error and a truncated file error? What format is syn4055334 = BM_10_652.unmapped.fq? Why is it some files are gzipped and others are not? Can the files be organized under directory folders according to what format they actually are? When I explore the STAR code provided at syn3219346, I see the parameter pass: --outReadsUnmapped fastx Need help and clarification on the above please. Thank you. Kory Johnson

Created by Kory Johnson johnsonko
Hi @johnsonko , All the files have been renamed and re-annotated to reflect the correct file format. Hope this helps!
Thanks for investigating this! I downloaded that file it's a gzipped fastq file. I will file an issue to rename these files to make that clear and so when downloading they are usable in a standard way. In terms of organization, all of these files are annotated (see https://docs.synapse.org/articles/annotation_and_query.html). This annotation includes `fileType`. We maintain a searchable table that includes these annotations for all files [here](https://www.synapse.org/#!Synapse:syn11346063/tables/). In your case, you might want fastq files from the MSBB study. This gives you that result in a fashion that you can download all of these files: ${synapsetable?query=SELECT %2A FROM syn11346063 WHERE %28 %28 "study" %3D %27MSBB%27 %29 AND %28 "assay" %3D %27rnaSeq%27 %29 AND %28 "fileFormat" %3D %27fastq%27 %29 %29&showquery=true}

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