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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