Update trimmomatic and HiSat2 parameters

NAL-i5K / NAL_RNA_seq_annotation_pipeline

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Update trimmomatic and HiSat2 parameters #32

Closed mpoelchau closed 4 years ago

mpoelchau commented 4 years ago

I think we can make the trimmomatic and hisat parameters more stringent than they currently are.

Change https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/blob/master/rnannot/RNAseq_annotate.py#L261 and similar lines to 'LEADING:30', 'TRAILING:30',
For the Hisat alignments, add --no-mixed and --no-discordant (eg. l. 149, 289, etc)

HsiuKangHuang commented 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'.

mpoelchau commented 4 years ago

Yes, please!

mpoelchau commented 4 years ago

@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.

mpoelchau commented 4 years ago

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'