Closed map2085 closed 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,
Update: --complement=no option has been made available since the commit 9626409.
--complement
option is missing again in the latest code?
Is it possible to use this option in the mapper?
No, I am afraid that the index has to be regenerated.
Thank you @smarco.
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.