dan_m

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dan_m
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Michigan USA
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Dan M

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  • It seems that the -nct and -nt options are not working in GATK 4 Pileup? gatk Pileup -nt 16 -nct 8 -R ref.fa -I my.bam -O my.pileup A USER ERROR has occurred: n is not a recognized option OOps nevermind .... Need to use the Spark version ht…
  • @Geraldine_VdAuwera said: Hi dan_m, we can't answer that for you, so I recommend you ask the author of STAR for help with this. He has an active mailing list: https://groups.google.com/forum/#!forum/rna-star Ok, FYI it turned out to be th…
  • Hi - I'm following this pipeline on some RNA samples, everything seems normal til I get to mapping against the generated splice junction reference with STAR. The final star alignments are 99% unmapped. Star log says: % of reads unmapped: too shor…