donkirkby
commented
8 years ago Here are the reference identifiers that Vera used in the checkMiSeq_refseqs_withoutHIVHCV.fasta file.
phiX174_sensulato_NC_001422 Ecoli_K-12_MG1655_NC_000913 Ecoli_RR1_CP011113 Pacnes_hdn-1_CP006032 GBvirusC_NC_001710 GBvirusB_NC_001655 HumanPegivirus2_NC_027998 HBV_ayw_NC_003977 MMLV_NC_001501 hg38_chr1 hg38_chr2 hg38_chr3 hg38_chr4 hg38_chr5 hg38_chr6 hg38_chr7 hg38_chr8 hg38_chr9 hg38_chr10 hg38_chr11 hg38_chr12 hg38_chr13 hg38_chr14 hg38_chr15 hg38_chr16 hg38_chr17 hg38_chr18 hg38_chr19 hg38_chr20 hg38_chr21 hg38_chr22 hg38_chrX hg38_chrY hg38_chrM hg38_chrUn_GL000195v1 hg38_chrUn_GL000213v1 hg38_chrUn_GL000214v1 hg38_chrUn_GL000216v2 hg38_chrUn_GL000218v1 hg38_chrUn_GL000219v1 hg38_chrUn_GL000220v1 hg38_chrUn_GL000224v1 hg38_chrUn_GL000226v1 hg38_chrUn_KI270302v1 hg38_chrUn_KI270303v1 hg38_chrUn_KI270304v1 hg38_chrUn_KI270305v1 hg38_chrUn_KI270310v1 hg38_chrUn_KI270311v1 hg38_chrUn_KI270312v1 hg38_chrUn_KI270315v1 hg38_chrUn_KI270316v1 hg38_chrUn_KI270317v1 hg38_chrUn_KI270320v1 hg38_chrUn_KI270322v1 hg38_chrUn_KI270329v1 hg38_chrUn_KI270330v1 hg38_chrUn_KI270333v1 hg38_chrUn_KI270334v1 hg38_chrUn_KI270335v1 hg38_chrUn_KI270336v1 hg38_chrUn_KI270337v1 hg38_chrUn_KI270338v1 hg38_chrUn_KI270340v1 hg38_chrUn_KI270362v1 hg38_chrUn_KI270363v1 hg38_chrUn_KI270364v1 hg38_chrUn_KI270366v1 hg38_chrUn_KI270371v1 hg38_chrUn_KI270372v1 hg38_chrUn_KI270373v1 hg38_chrUn_KI270374v1 hg38_chrUn_KI270375v1 hg38_chrUn_KI270376v1 hg38_chrUn_KI270378v1 hg38_chrUn_KI270379v1 hg38_chrUn_KI270381v1 hg38_chrUn_KI270382v1 hg38_chrUn_KI270383v1 hg38_chrUn_KI270384v1 hg38_chrUn_KI270385v1 hg38_chrUn_KI270386v1 hg38_chrUn_KI270387v1 hg38_chrUn_KI270388v1 hg38_chrUn_KI270389v1 hg38_chrUn_KI270390v1 hg38_chrUn_KI270391v1 hg38_chrUn_KI270392v1 hg38_chrUn_KI270393v1 hg38_chrUn_KI270394v1 hg38_chrUn_KI270395v1 hg38_chrUn_KI270396v1 hg38_chrUn_KI270411v1 hg38_chrUn_KI270412v1 hg38_chrUn_KI270414v1 hg38_chrUn_KI270417v1 hg38_chrUn_KI270418v1 hg38_chrUn_KI270419v1 hg38_chrUn_KI270420v1 hg38_chrUn_KI270422v1 hg38_chrUn_KI270423v1 hg38_chrUn_KI270424v1 hg38_chrUn_KI270425v1 hg38_chrUn_KI270429v1 hg38_chrUn_KI270435v1 hg38_chrUn_KI270438v1 hg38_chrUn_KI270442v1 hg38_chrUn_KI270448v1 hg38_chrUn_KI270465v1 hg38_chrUn_KI270466v1 hg38_chrUn_KI270467v1 hg38_chrUn_KI270468v1 hg38_chrUn_KI270507v1 hg38_chrUn_KI270508v1 hg38_chrUn_KI270509v1 hg38_chrUn_KI270510v1 hg38_chrUn_KI270511v1 hg38_chrUn_KI270512v1 hg38_chrUn_KI270515v1 hg38_chrUn_KI270516v1 hg38_chrUn_KI270517v1 hg38_chrUn_KI270518v1 hg38_chrUn_KI270519v1 hg38_chrUn_KI270521v1 hg38_chrUn_KI270522v1 hg38_chrUn_KI270528v1 hg38_chrUn_KI270529v1 hg38_chrUn_KI270530v1 hg38_chrUn_KI270538v1 hg38_chrUn_KI270539v1 hg38_chrUn_KI270544v1 hg38_chrUn_KI270548v1 hg38_chrUn_KI270579v1 hg38_chrUn_KI270580v1 hg38_chrUn_KI270581v1 hg38_chrUn_KI270582v1 hg38_chrUn_KI270583v1 hg38_chrUn_KI270584v1 hg38_chrUn_KI270587v1 hg38_chrUn_KI270588v1 hg38_chrUn_KI270589v1 hg38_chrUn_KI270590v1 hg38_chrUn_KI270591v1 hg38_chrUn_KI270593v1 hg38_chrUn_KI270741v1 hg38_chrUn_KI270742v1 hg38_chrUn_KI270743v1 hg38_chrUn_KI270744v1 hg38_chrUn_KI270745v1 hg38_chrUn_KI270746v1 hg38_chrUn_KI270747v1 hg38_chrUn_KI270748v1 hg38_chrUn_KI270749v1 hg38_chrUn_KI270750v1 hg38_chrUn_KI270751v1 hg38_chrUn_KI270752v1 hg38_chrUn_KI270753v1 hg38_chrUn_KI270754v1 hg38_chrUn_KI270755v1 hg38_chrUn_KI270756v1 hg38_chrUn_KI270757v1 Pdenitrificans_PD1222_chr1_NC_008686 Pdenitrificans_PD1222_plasmid1_NC_008688 Pdenitrificans_PD1222_chr2_NC_008687
Add a few more references to the preliminary mapping step for things like phiX and E. coli.
Display a graph for each sample showing the relative amounts of target genomes and contaminants. Calculate the portions just based on read counts.
Make the remap step exclude any projects without coordinate references. That way we will calculate the portions of contaminants, but we won't carry them through the remapping and coverage steps.
Vera posted some example code on GitHub.