Hi all, I am very new to working with sequencing data and have run into a problem when using SAMtools to sort some of my larger files. When running the following
samtools sort Sample_aligned.bam > Sample_aligned_sorted.bam this error will be returned Failed to open file ./samtools.7711.2619.tmp.0252.bam samtools sort: fail to open "./samtools.7711.2619.tmp.0252.bam”: Too many open files This error only occurs when trying to sort larger .bam files. I am working locally to avoid running on a cluster, and was wondering if there is a way to split the large .bam files that does not rely on chromosomal information (I do not have this information in my reference transcriptome). My initial idea is to split the original .bam file into 2, sort each file, and then concatenate them with the goal of preserving the sort. Is there a way to do this without creating additional problems downstream (example: not splitting the files by line number and instead using a different metric)? Best, Fauna
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