I am trying to quantify the expression of my genes by using salmon.
The command is following
salmon quant -p 10 -i ensembl_index/ -l A -1 SRR1056045_2.fastq.gz -2 SRR1056045_1.fastq.gz -o ensembl_quant
But got the following error message:
Error reading from the FASTA/Q stream. Minimum return code for left and right read was (-2). Make sure the file is valid.
I was trying to analyse 5 .sra files which were downloaded from ncbi. Two of my files were OK, but enter-count problems with rest three. Same error message for them. Is it the problem with those .sra files?