Hello. I'm having issues with Cuffdiff and can not figure out why. The program says the read order has to be the same but I ran all of then with Samtools sort -n to make sure and still having that issue.
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You need to sort by coordinate, not by name (remove the -n flag). The header of the bam should look something like this afterward:
@HD VN:1.0 SO:coordinate -
So do I sort the bam files using @HD VN:1.0 SO:coordinate with samtools?Originally posted by Brian Bushnell View PostComment
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No that is how the first header line should look after sorting.
Just remove -n option when you sort with samtools like Brian said.Comment
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You can check the headers of the BAM files with samtools view.
Code:samtools view -H fileName.bam
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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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