I have uploaded the CSHL Long RNA-seq fastq dataset from the UCSC genome browser to galaxy and attempted to map the reads using bowtie, bwa and tophat. None of them are able to align more than a super small fraction of the reads. I have used each of these programs to align exactly the same types fastq data before, and it has worked perfectly. Does anyone have any suggestions as to what the problem could be?
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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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