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smarco / gem3-mapper

GEM-Mapper v3
GNU General Public License v3.0
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No more "--complement" option? #1

Closed map2085 closed 6 years ago

map2085 commented 6 years ago

I am excited to see renewed maintenance and development of GEM. It is the only aligner I can trust to report all alignments for each read within given error thresholds.

In the GEM Beta build 1.376 (beta) - (2013/04/06 02:13:06 GMT), there was an option in the indexer for "--complement no" which would force mapping reads to the forward strand only. This is useful for Stranded RNA-seq data, which is very common nowadays.

I do not see the "--complement" option in GEMv3.
How can I make GEMv3 do strand-specific mapping?

Thank you.

smarco commented 6 years ago

Good to hear that.

The point is that I didn't had the feeling that no-complement index option was being used. But, if that is the case, I can easily push an update to support it again.

Thanks for the feedback. Best,

smarco commented 6 years ago

Update: --complement=no option has been made available since the commit 9626409.

y9c commented 2 months ago

--complement option is missing again in the latest code?

smarco commented 2 months ago

Hi,

There should be the option on the gem-indexer at here.

y9c commented 2 months ago

Is it possible to use this option in the mapper?

smarco commented 2 months ago

No, I am afraid that the index has to be regenerated.

y9c commented 2 months ago

Thank you @smarco.