Biostar Beta. Not for public use.
Question: Salmon error message
Entering edit mode

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?


ADD COMMENTlink 16 months ago saadleeshehreen • 60 • updated 16 months ago Devon Ryan 90k
Entering edit mode

If you are worried about sra files, you can directly download your fastq.gz files here:

ADD REPLYlink 16 months ago
• 480
Entering edit mode

A couple things:

  1. One of those files (likely SRR1056045_1.fastq.gz) is corrupt. Just download it again.
  2. You flipped which file goes where. The _1 file should be with -1 and the _2 file should be with -2. Granted, salmon may figure out you've swapped things since you specified -l A, but there's no need to chance that.
ADD COMMENTlink 16 months ago Devon Ryan 90k

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.0