Hello, I have a bam file formatting issue.
samtools-0.1.18 (Linux) shows the bam to contain 875 reads mapped. [cid:c32e9022-0c2c-4630-85ab-c9d4ce1f4bf9] I've run featureCounts, a software module of Subread (http://subread.sourceforge.net/) to count the number of read mapped per CDS to a reference genome. The program only processes 116 reads for this bam (rather than the expected 875), and suggests truncation or missing data. [cid:5abca696-b95f-4911-a199-37a47ebf33db] Can someone help debug the formatting issue? Workflow to create the bam file is as follows: -De novo assembly of reads in CLC Workbench -Bowtie2 to map reads against reference genome -Pipe to samtools to generate bam and sort file by coordinate -Run in featureCounts ./bowtie2 -x bact_contigs -f -a -t --no-unal -p 36 s1_assembly.fasta | ~/samtools-0.1.18/samtools view -Shu - | ~/samtools-0.1.18/samtools sort -m 5000000000 - s1_sortcoord I've re-generated the bam files with and without piping to samtools, and versions of both software, but still get the same error. Also, below is a file size comparison for the file and its index. [cid:32f4bea4-956a-4a56-9b26-26c8ef290ecc] --- Thanks, Camille Daniels, Ph.D. Post Doctoral Fellow Red Sea Research Center Al-Haytham West (Building 2), Room 2227-WS02 Thuwal, Saudi Arabia 23599-6900 [email protected] Office: +966 02 808 2446 --- ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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