How to ensure that the read names are identical except for /1 or /2

Question

[hydra_questions]

I am trying to do a de novo transcriptome with paired-end reads using Trinity. I have received the following error:

 pairs.K25.stats is empty.  Be sure to check your fastq reads and ensure that the read names are identical except for th
e /1 or /2 designation. at /usr/local/trinity/trinityrnaseq-Trinity-v2.4.0/util/insilico_read_normalization.pl line 904.
CMD finished (38 seconds)

My files are quite large and I'm using quite a few, I was wondering if anyone had any advice on how to identify where this error is originating from without manually scanning all of my files

Answer 1

[hydra_questions]

I manually looked through each read using:

head read1.fq
head read2.fq

I did this for each pair & noticed one pair were both coded as read 1. I observed the contents of the sample file throughout the preprocessing steps, saw where the error occurred and applied all the necessary changes from that point. I ran trinity again with no problems.

[GenoMax]

You should have used a utility like repair.sh from BBTools. It is not practical to manually inspect things like large sequence data files.