Question: featureCounts error with 150bp Paired end RNA seq data
0
gravatar for ankuresearch
3 months ago by
ankuresearch10
ankuresearch10 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 11 weeks ago by swbarnes27.0k • written 3 months ago by ankuresearch10
2
gravatar for ATpoint
3 months ago by
ATpoint25k
Germany
ATpoint25k wrote:

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

ADD COMMENTlink written 3 months ago by ATpoint25k
0
gravatar for swbarnes2
11 weeks ago by
swbarnes27.0k
United States
swbarnes27.0k wrote:

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

ADD COMMENTlink written 11 weeks ago by swbarnes27.0k
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