featureCounts error with 150bp Paired end RNA seq data

Question

[Ankur B. Sharma]

Hi everyone, I am new to Linux based data analysis. I am using Subread package fetaureCounts to count the number of reads. I am using bam files (obtained after aligning fastq files to mm10 using STAR) as input files for featureCounts but facing this error. Please help me in troubleshooting this error.

Data type: 150bp Paired-end RNA seq data, aligned to mm10 using STAR aligner

Script: featureCounts -s 1 --primary -p -T 5 -t exon -g gene_id -a gencode.vM19.annotation.ERCC92.gtf -o files_rep1_02_08_19_counts.vM19.ERCC92.txt file1_star_mm10_trimmed_fastqfilesAligned.sortedByCoord.out.bam file2_star_mm10_trimmed_fastqfilesAligned.sortedByCoord.out.bam file3_star_mm10_trimmed_fastqfilesAligned.sortedByCoord.out.bam file4_star_mm10_trimmed_fastqfilesAligned.sortedByCoord.out.bam file5_star_mm10_trimmed_fastqfilesAligned.sortedByCoord.out.bam

Error:
featureCounts: input-files.c:4571: SAM_pairer_finish_margins: Assertion `Sbin' failed.
featureCounts.ercc.sh: line 1: 21579 Aborted                 (core dumped)

Answer 1

[ATpoint]

See https://groups.google.com/forum/#!topic/subread/g3JT6XReht0, try upgrade to current (most recent) version.

Answer 2

[swbarnes2]

For troubleshooting, why don't you try giving the software one bam at a time?