Using RSem of Trinity, align_and_estimate_abundance.pl script, all folders for sample/condition is not being created

Question

[Roy.anupama11]

Hi,

Folders for all the samples are not being created, only 1/4 is created using align_and_estimate_abundance.pl script provided by Trinity, is giving output.

What to do? What must be the error? Can I run the script for each sample/ condition separately?

Thank you. Hope to get a response soon

Anupama

[ATpoint]

Error, fewer reads in file specified with -2 than in file specified with -1

That's pretty clear is it? Some of your fastq file pairs are out of sync. Did you do any manipulation like trimming of paired-end data with a non paired-end aware tool? Please describe how data were obtained and processed before running that analysis here.

[Roy.anupama11]

Firstly thank you for responding. I did trimming for adapter sequences using Trimmomatic. In the script for quantification, I am using only trimmed paired end data, leaving the upaired data formed after trimming. I have used HISAT2, then STRINGTIE and TRINITY for preparing reference.

[ATpoint]

In the script for quantification, I am using only trimmed paired end data, leaving the upaired data formed after trimming.

What does that mean? Please show code. In any case, unpaired data should be gone after the trimming as this is exactly what causes this issue here. The tool expects paired data, no singleton reads.