Is the output bam file already sorted and indexed? If not, how can I index this file on galaxy? I cannot find the samtool index tool.
Hi @DHowell23
By default, BAM files produced in Galaxy are sorted by coordinate and indexed. “Bowtie2”, just like other aligners in Galaxy, is a pipeline containing several tools including samtools sort. Click at Info ( i ) icon and check command box to see the tools used for the job. Click at Preview (eye) icon for any BAM file with aligned reads. The first line in the header describes sorting. You should see something like: SO:coordinate. Click at Donwload icon (floppy disc) for any BAM file with aligned reads. You’ll see a small menu: Download dataset and Download bam_index.
Kind regards,
Igor
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