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ncapSeekerConfigure_hg38.xml
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ncapSeekerConfigure_hg38.xml
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<?xml version="1.0"?>
<configure>
<splicingDir_V30>/public/home/huangjh/genome/human/hg38/annotations/gencodeV30/annotationSite/splicing</splicingDir_V30>
<exonAnnotation_rmMiRNA>/public/home/huangjh/genome/human/hg38/annotations/gencodeV30/annotationBed/hg38.genecode.v30.tRNA.snoRNA.miRNA.rmsk.chrM.RefseqNcrna.upDwStream.curated.exonFeatures.rmMiRNA.bed6</exonAnnotation_rmMiRNA>
<rriScan>/public/home/huangjh/bioTools/bin/rriScan</rriScan>
<rriScanParameter>-l 15 -M 0 -p 0 -s 5 -g 1</rriScanParameter>
<starParameter_rriScan>--runThreadN 16 --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --outFilterType Normal --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 0 --alignIntronMin 3 --scoreGapNoncan -2 --scoreGapATAC -2 --scoreGapGCAG -2 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimMultimapNmax 30 --chimMultimapScoreRange 2 --chimScoreJunctionNonGTAG -8 --alignSJoverhangMin 15 --alignSJDBoverhangMin 10 --chimOutType Junctions --outSAMtype BAM SortedByCoordinate --outSAMmode Full --outSAMattributes All --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --limitOutSJcollapsed 5000000 --outReadsUnmapped Fastx --readFilesCommand zcat</starParameter_rriScan>
<intronScan>/public/home/huangjh/bioTools/bin/intronScan</intronScan>
<intronScanParameter>--norm --pair</intronScanParameter>
<trimScan>/public/home/huangjh/bioTools/bin/trimScan</trimScan>
<trimScanParameter>--onlyPE --nap</trimScanParameter>
<scanMotif>/public/home/huangjh/bioTools/bin/scanMotif</scanMotif>
<scanMotifParameter>-s 0.7</scanMotifParameter>
<motifMatrix>/public/home/huangjh/perlBioTools/scanMotif/manual_correct_motifs.motif</motifMatrix>
<motifMatrix_pol3>/public/home/huangjh/perlBioTools/scanMotif/pol3Motif.motif</motifMatrix_pol3>
<rnaMotifSeeker>/public/home/huangjh/bioTools/bin/rnaMotifSeeker</rnaMotifSeeker>
<rnaMotifSeekerParameter>--norc</rnaMotifSeekerParameter>
<genomeFile>/public/home/huangjh/genome/human/hg38/hg38.fa</genomeFile>
<faidxFile>/public/home/huangjh/genome/human/hg38/hg38.fa.fai</faidxFile>
<exonAnnotation>/public/home/huangjh/genome/human/hg38/annotations/gencodeV30/annotationBed/hg38.genecode.v30.tRNA.snoRNA.miRNA.rmsk.chrM.RefseqNcrna.curated.exonFeatures.bed6</exonAnnotation>
<exonAnnotation_revisedSnoRA37AB>/public/home/huangjh/genome/human/hg38/annotations/gencodeV30/annotationBed/hg38.genecode.v30.tRNA.snoRNA.miRNA.rmsk.chrM.RefseqNcrna.curated.exonFeatures.revisedSnoRA37AB.bed6</exonAnnotation_revisedSnoRA37AB>
<geneGtf>/public/home/huangjh/genome/human/hg38/annotations/gencodeV30/originalData/hg38.gencode.v30.annotation.gtf</geneGtf>
<annotationDir>/public/home/huangjh/genome/human/hg38/annotations/gencodeV30/annotationSite/common</annotationDir>
<ncrnaDir>/public/home/huangjh/genome/human/hg38/annotations/gencodeV30/annotationSite/ncRNA</ncrnaDir>
<splicingDir_2>/public/home/huangjh/genome/human/hg38/annotations/gencodeV30/annotationSite/splicing/1</splicingDir_2>
<splicingDir>/public/home/huangjh/genome/human/hg38/annotations/gencodeV30/annotationSite/splicing</splicingDir>
<RNAmodDir>/public/home/huangjh/genome/modSites</RNAmodDir>
<modSite>/public/home/huangjh/genome/modSites/human/human.hg38.allMod.result.col29.bed6</modSite>
<conservationProfile>/public/home/huangjh/genome/human/hg38/conservation/hg38.phyloP100way.bw</conservationProfile>
<starProgram>/public/home/huangjh/softwares/STAR/bin/STAR</starProgram>
<starParameter>--runThreadN 16 --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15 --outFilterMatchNminOverLread 0.8 --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 20 --alignSJDBoverhangMin 10 --outSAMtype BAM Unsorted --outSAMmode Full --outSAMattributes All --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --limitOutSJcollapsed 5000000 --alignEndsProtrude 150 ConcordantPair --readFilesCommand zcat</starParameter>
<chainDir>/public/home/huangjh/genome/chainFile/hg38</chainDir>
<starParameter_nonZcat>--runThreadN 16 --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --alignEndsType Local --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 20 --outFilterMatchNminOverLread 0.8 --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 20 --alignSJDBoverhangMin 10 --outSAMtype BAM Unsorted --outSAMmode Full --outSAMattributes All --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --limitOutSJcollapsed 5000000 --alignEndsProtrude 150 ConcordantPair</starParameter_nonZcat>
<genomeSeqDir>/public/home/huangjh/genome/WholeGenomeFasta</genomeSeqDir>
<modificationSite>/public/home/huangjh/genome/modSites/human_all_RNA_modification_sites.bed6</modificationSite>
<RbsSite>/public/home/huangjh/genome/rbsSites/hg38_all_CLIP_peaks_sorted.bed</RbsSite>
<starIdx>/public/home/huangjh/genome/human/hg38/indexes/StarIndex/</starIdx>
<starIdx_napRNAs>/public/home/huangjh/genome/human/hg38/indexes/StarNewIndex/napRNAs/</starIdx_napRNAs>
<starParameterAlignEndsTypeLocal>--runThreadN 16 --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --alignEndsType Local --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 20 --outFilterMatchNminOverLread 0.8 --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 20 --alignSJDBoverhangMin 10 --outSAMtype BAM Unsorted --outSAMmode Full --outSAMattributes All --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --limitOutSJcollapsed 5000000 --alignEndsProtrude 150 ConcordantPair --readFilesCommand zcat</starParameterAlignEndsTypeLocal>
<starParameter_shapemapper>--runThreadN 16 --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --alignEndsType Local --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 20 --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 20 --alignSJDBoverhangMin 10 --outSAMmode Full --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --limitOutSJcollapsed 5000000 --alignEndsProtrude 150 ConcordantPair --readFilesCommand zcat --scoreGap -1000000 --scoreDelBase -1 --scoreInsBase -1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 999 --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMattributes MD --outFilterMatchNminOverLread 0</starParameter_shapemapper>
<starParameter_zhangQiangFeng_icSHAPE>--runThreadN 16 --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 20 --outFilterMatchNminOverLread 0.8 --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 20 --alignSJDBoverhangMin 10 --outSAMmode Full --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --limitOutSJcollapsed 5000000 --alignEndsProtrude 150 ConcordantPair --readFilesCommand zcat --outFilterMismatchNmax 3 --outFilterMultimapNmax 10 --alignEndsType Local --scoreGap -1000 --outSAMmultNmax 1</starParameter_zhangQiangFeng_icSHAPE>
<ncapSeeker>/public/home/huangjh/bioTools/bin/ncapSeeker</ncapSeeker>
<ncapSeekerParameter>-t 5 -c 2 -F 2 -e 5 -s --norm --pair</ncapSeekerParameter>
<ncapSeekerParameter_nanopore>-t 5 -c 2 -F 2 -e 5 -s --norm</ncapSeekerParameter_nanopore>
<startEndSeeker>/public/home/huangjh/bioTools/bin/napEndSeeker</startEndSeeker>
<startEndSeekerParameter>-s -t 2 -m 2</startEndSeekerParameter>
<bedConservation>/public/home/huangjh/bioTools/bin/bedConservation</bedConservation>
<bedConservationParameter>-c -1000</bedConservationParameter>
<bedAnnotator>/public/home/huangjh/bioTools/bin/bedAnnotator</bedAnnotator>
<bedAnnotatorParameter>-s 1</bedAnnotatorParameter>
<bedAnnotatorParameter2>-s 0</bedAnnotatorParameter2>
<bedtools>/public/home/huangjh/softwares/DOTSF/bedtools-2.17.0/bin/bedtools</bedtools>
<bedtools2>bedtools</bedtools2>
<samtools>/public/home/huangjh/softwares/samtools/samtools</samtools>
<ncapToWig>/public/home/huangjh/bioTools/bin/ncapToWig</ncapToWig>
<ncapToWigParameter>-s --ncap --rpm -P --norm</ncapToWigParameter>
<ncapToWigParameter2>-s --ncap --rpm --norm</ncapToWigParameter2>
<wigToBigWig>/public/home/huangjh/softwares/kentUcscExe/wigToBigWig</wigToBigWig>
<chromSizeFile>/public/home/huangjh/softwares/kentUcscExe/hg38.chrom.sizes</chromSizeFile>
<annotateSites>/public/home/huangjh/bioTools/bin/annotateSites</annotateSites>
<annotateSitesParameter>-s -m 0.0001 -w 50</annotateSitesParameter>
<drawAnnotateSites>/public/home/huangjh/perlBioTools/annotateSite/drawAnnotateSites.R</drawAnnotateSites>
<findMotifSite>/public/home/huangjh/perlBioTools/novelClassNcRNA/findSigPosMotifs.pl</findMotifSite>
<bamExpression>/public/home/huangjh/C/bin/bamExpression</bamExpression>
<bamExpressionr_yang_NAP>/public/home/huangjh/bioTools/bin/bamExpression</bamExpressionr_yang_NAP>
<bamExpressionParameter>--noSplice --norm</bamExpressionParameter>
<bamExpressionParameter_yang_NAP>--pair --noSplice --norm</bamExpressionParameter_yang_NAP>
<bamToWig>/public/home/huangjh/C/bin/bamToWig</bamToWig>
<bamToWigParameter>-s --norm --rpm</bamToWigParameter>
<bamToWigParameter_1>-s --norm --rpm</bamToWigParameter_1>
<diffExp>/public/home/huangjh/perlBioTools/ncapSeeker/limmaRNAseqDiffExp.R</diffExp>
<liftOver>/public/home/huangjh/softwares/kentUcscExe/liftOver</liftOver>
<liftOverParameter>-minMatch=0.8</liftOverParameter>
<clustalw>/public/home/huangjh/softwares/clustalw/clustalw2</clustalw>
<r2r>/public/home/huangjh/softwares/R2R-1.0.6/bin/r2r</r2r>
<rscape>/public/home/huangjh/softwares/rscape_v1.5.16/bin/R-scape</rscape>
<RNAalifoldParameter>--noPS --aln-stk=</RNAalifoldParameter>
<rscapeParameter>--rna --fold -s --r2rall</rscapeParameter>
<rscapeParameter_old>--rna -s --r2rall --gapthresh 1 -E 0.05</rscapeParameter_old>
<circos>/public/home/huangjh/softwares/circos/bin/circos</circos>
<featureCounts>/public/home/huangjh/softwares/subread/bin/featureCounts</featureCounts>
<featureCountsParameter>-T 16 -M --fraction -p -d 15 -D 10000</featureCountsParameter>
</configure>