Closed mpoelchau closed 4 years ago
Do I also need to change 'LEADING:3', 'TRAILING:3'
to 'LEADING:30', 'TRAILING:30'
in line 102, 115 and 128?
The option of trimmomatic_jar in these three lines is 'SE', not 'PE'.
Yes, please!
@HsiuKangHuang for testing purposes, can you generate another Tribolium file (from the same SRR as before) with trimmomatic parameters 'LEADING:3', 'TRAILING:3'? No need to change the code on the branch yet, but it would be great to see what differences there are.
Thanks @HsiuKangHuang! The mapping looks better with the older parameters (see for example https://apollo-dev.nal.usda.gov/apollo-2.6.0/1250977/jbrowse/index.html?loc=NC_007425.3%3A4199750..4218249&tracks=DNA%2CAnnotations%2Ctricas_current_models%2CTricas_Tcas5.2_RNA-Seq-alignments_2020-05-20_coverage%2CTricas_Tcas5.2_RNA-Seq-alignments_2020-05-31_coverage&highlight=), so let's stick with LEADING:30', 'TRAILING:30'
I think we can make the trimmomatic and hisat parameters more stringent than they currently are.
'LEADING:30', 'TRAILING:30',
--no-mixed
and--no-discordant
(eg. l. 149, 289, etc)