I am having hard time to get SAM output from Bowtie. Anybody know the command?? bowtie manual says -S/--sam but I don't know how to use it. please suggest me complete mommand.
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just add the -S to the command.
Eg:
$bowtie -S --fr reference.build -1 inputreadspair1.fastq -2 inputreadspair2.fastq output.sam -
thanks shophied, I tried, it gives me output but when I tried to convert that sam file to bam it says header is missing from sam!!Comment
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Did you run bowtie with --sam-nohead or --sam-nosq? I imagine either of those could lead to that sort of error message.Comment
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I am trying to get a plot of DNA repeats that can serve as a figure for my paper. Is there a good program to find the repeat on genome and give output as heatmap or other sorts of plot.
The genomic region i want to analyze is 9 mbComment
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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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