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Old 02-14-2014, 04:27 AM   #1
Location: Norway

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Default Mapping stranded smallRNA reads with TopHat


I have short reads (max 50 nts, mostly 20-40 nts) that are from a stranded ligated Illumina library. I could't find if Bowtie2 has a stranded option so I use the TopHat fr-secondstrand option. But I don't expect my reads to be spliced so is there an option to skip the read segmentation? Or should I use other mappers for this job?


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Old 02-14-2014, 05:05 AM   #2
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You can try the subread aligner and featureCounts downstream.
GenoMax is offline   Reply With Quote

bowtie 2, mapping, small rna, tophat 2

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