In syn8612191, many of the samples are missing. Also, I have to say that fastq.gz files in syn7416949 have serious issues with the number of reads. If you convert Bam files to fastq files you can see that its better either to download Bam files and then convert them to fastq files or download files from syn8612191 but there many samples missing. Would you please check it and provide all the samples?
Thanks
Created by Iman Sadeghi Isadeghi66 The fastq files in syn7416949 only have the unmapped reads. These were provided in addition to the bam files to facilitate recreating the full fastq. As you have discovered the rnaSeqReprocessing study has fastq that were generated by doing that. These are the files from MSBB that were used in the x-consortium analysis.