Hello,
Thank you for the tool !
I am trying to use salsa2 to scaffold my assembly (70X of HiC data),
I performed mapping and processing following Arima pipeline (I just changed to MapQ > 20 instead of 10),
Scaffolding seem to work but they are clearly some contigs that could be "grouped" and are not (see the heatmap attached). The more iterations the software does the more contigs are grouped, so I would like to incease the number of iteration. However as mentionned elsewhere on this git the number of iteration can't be controlled anymore.
Can you help me ? Is there a way to prevent salsa to stop iterating a bit too soon for example ?
Thank you very much !
Vincent
This is related to #151 (comment).
Hello,
Thank you for the tool !
I am trying to use salsa2 to scaffold my assembly (70X of HiC data),
I performed mapping and processing following Arima pipeline (I just changed to MapQ > 20 instead of 10),
Scaffolding seem to work but they are clearly some contigs that could be "grouped" and are not (see the heatmap attached). The more iterations the software does the more contigs are grouped, so I would like to incease the number of iteration. However as mentionned elsewhere on this git the number of iteration can't be controlled anymore.
Can you help me ? Is there a way to prevent salsa to stop iterating a bit too soon for example ?
Thank you very much !
Vincent
This is related to #151 (comment).