How to figure out if two reads (with STAR) are consistent?

[InquilineKea]

So as a sample command, I tried this below:

STAR --genomeDir /home/simfish/Desktop/RNAseq/ --readFilesIn SRR925687_1.fastq SRR925688_1.fastq --outFilterMultimapNmax 1 --outSAMstrandField intronMotif --sjdbGTFfile /home/simfish/Desktop/RNAseq/Homo_sapiens.GRCh38.76.gtf --outFileNamePrefix /home/simfish/Desktop/ --runThreadN 32

==

But this resulted in a fatal error described below:

EXITING because of FATAL ERROR: Read1 and Read2 are not consistent, reached the end of the one before the other one
SOLUTION: Check you your input files: they may be corrupted

Mar 12 19:45:21 ...... FATAL ERROR, exiting

==

Is there a way to check the reads for consistency prior to running STAR on them? I'm new to STAR and I'm trying the tutorial over at http://www.genefriends.org/RNAseqForDummies/ - there is an issue with the last step (wrt running STAR). I'd like to select a pair of reads that could produce meaningful interpretable results.

[Brian Bushnell]

This is not a problem with Star; rather, it's good that Star notified you of the problem!

SRR925687_1.fastq
SRR925688_1.fastq

It looks like you are trying to treat read1 from two different libraries as pairs - you can't do that! To map reads as pairs, the must come from the same library and be in the same order. Possibly, SRR925687_1.fastq and SRR925687_2.fastq would go together, if SRR925687_2.fastq exists.

SRA files are notoriously annoying to deal with - you may want to post the exact command line you used when converting them to fastq.

If the read headers are retained properly by the SRA software, you can run Reformat on them like this to ensure they appear to be correctly paired:

reformat.sh in1=reads1.fastq in2=reads2.fastq vpair

This will look at the read names and tell you whether they match; they will, only if they are correctly paired Illumina files with their original names.

Edit: cross-posted here