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
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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
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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.
SRR925687_1.fastq
andSRR925688_1.fastq
are not paired end fastq files. You should align them separately. The aligner is assuming them to be part of the same pair and complaining as these files have different number of reads.