Question

1-based coordiante system for sam files

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9.8 years ago

Whoknows ▴ 960

Hi

How can I set 1-based coordinate system for my bowtie output sam files?

thanks a lot,

sam bowtie • 1.6k views

ADD COMMENT • link updated 2.5 years ago by Ram 43k • written 9.8 years ago by Whoknows ▴ 960

Ram · Answer 1 · 2014-06-30

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9.8 years ago

Devon Ryan 104k

SAM files are always 1-based (BAM is 0-based).

ADD COMMENT • link updated 2.5 years ago by Ram 43k • written 9.8 years ago by Devon Ryan 104k

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thanks, and what is the parameter for bowtie?

ADD REPLY • link 9.8 years ago by Whoknows ▴ 960

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ADD REPLY • link 9.8 years ago by Devon Ryan 104k

Ram · Answer 2 · 2014-07-01

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9.8 years ago

Whoknows ▴ 960

I found the bowtie option , you should to set -B 1 for 1-based coordinate system

ADD COMMENT • link updated 2.5 years ago by Ram 43k • written 9.8 years ago by Whoknows ▴ 960

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That's only for the old bowtie format, which should never be used anymore. SAM format is always 1-based.

ADD REPLY • link updated 2.5 years ago by Ram 43k • written 9.8 years ago by Devon Ryan 104k