SplitNCigar with draft assembly?
Hi, I'm trying to use the RNAseq best practices to call SNPs in transcriptomes aligned to a draft assembly for a non-model species. Everything has worked fine so far, but when I try to use SplitNCigar it doesn't seem to filter anything:
INFO 14:09:51,596 ProgressMeter - Total runtime 961.86 secs, 16.03 min, 0.27 hours
INFO 14:09:51,598 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 21140216 total reads (0.00%)
INFO 14:09:51,599 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 14:09:51,599 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 14:09:51,599 MicroScheduler - -> 0 reads (0.00% of total) failing ReassignOneMappingQualityFilter
Done. There were no warn messages.
Is this because my genome lacks annotations? Is there a way to use the splice junctions inferred by STAR? It seems improbable that not a single read was filtered. (Before this, I aligned the raw reads with STAR 2-pass and ran the Picard steps CleanSam, AddOrReplaceReadGroups and Mark Duplicates).
Thanks so much!