Question: featureCounts error with 150bp Paired end RNA seq data
0
gravatar for Ankur B. Sharma
6 months ago by
Nanyang Technological University, Singapore
Ankur B. Sharma10 wrote:

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)
ADD COMMENTlink modified 5 months ago by swbarnes27.4k • written 6 months ago by Ankur B. Sharma10
2
gravatar for ATpoint
6 months ago by
ATpoint29k
Germany
ATpoint29k wrote:

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

ADD COMMENTlink written 6 months ago by ATpoint29k
0
gravatar for swbarnes2
5 months ago by
swbarnes27.4k
United States
swbarnes27.4k wrote:

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

ADD COMMENTlink written 5 months ago by swbarnes27.4k
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