I just started working on TCGA high-throughput RNA-Seq data from SRA (short read archive). I was trying to convert lite.sra files to fastq format usign sra-toolkit's fastq-dump utility that I downloaded couple of months ago. It seems the older binary files are not working properly on the data from TCGA.
Anyone who is also facing the same problem, please update your sra toolkit binary files to version 2.1.9 that works very well with the TCGA data.
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