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!

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Answers

  • J_RJ_R NCMember

    Thanks so much, that's extremely helpful. I clearly should have read the instructions more carefully. Thanks again!

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