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epifluidlab / FinaleMe

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where the *WGS.FinaleMe.mincg7.mergerd.cov.37.bw and autosome_1kb_intervals.UCSC.cpgIsland_plus_shore.b37.bed file if from? #6

Open biwdpang opened 3 months ago

biwdpang commented 3 months ago

Hi, it is a good work!

I hvae done the step1-4 sucessful, but what is the *WGS.FinaleMe.mincg7.mergerd.cov.37.bw. I can't see the file from where.

"ls *WGS.FinaleMe.mincg7.merged.cov.b37.bw | perl -ne 'chomp;$cov=$_;$m=$cov;$m=~s/cov/methy_count/;print " -bigWig $m -useMean0 0 -regionMode 0 -bigWig $cov -useMean0 0 -regionMode 0";' >> cfdna.methy_summary.cmd.txt"

And, can perl open the bigwig file directly?

Addition, where can i get the autosome_1kb_intervals.UCSC.cpgIsland_plus_shore.b37.bed file about next step

"perl -e '$cmd=cat cfdna.methy_summary.cmd.txt;chomp($cmd); java -Xmx10G -cp "lib/dnaaseUtils-0.14-jar-with-dependencies.jar:lib/java-genomics-io.jar:lib/igv.jar" main.java.edu.mit.compbio.utils.AlignMultiWigInsideBed autosome_1kb_intervals.UCSC.cpgIsland_plus_shore.b37.bed output.add_value.methy.bed.gz $cmd;'"

heweihuang commented 2 months ago

May I ask how you ran the second step? I encountered an error when running the second step, could you provide the relevant executable file? Thank you.

TongZhou202103 commented 1 month ago

May I ask how you ran the second step? I encountered an error when running the second step, could you provide the relevant executable file? Thank you.

Did you encounter the error ‘0 is smaller than, or equal to, the minimum (0)’? Have you solved it?

biwdpang commented 3 weeks ago

Hi, this is the step1-3 running command.

Step 1: extract features from bam files for the training and decoding

step1_max_memory="20G"

cd $outdir &&\

java -Xmx40G -cp "$FinaleMe/FinaleMe-0.58-jar-with-dependencies.jar:$FinaleMe/lib/gatk-package-distribution-3.3.jar:$FinaleMe/lib/sis-jhdf5-batteries_included.jar:$FinaleMe/lib/java-genomics-io.jar:$FinaleMe/lib/igv.jar" \ org.cchmc.epifluidlab.finaleme.utils.CpgMultiMetricsStats \ $hg38_2bit $cpgsite $cpgsite $input_bam $outdir/CpgMultiMetricsStats.hg38.details.bed.gz \ -stringentPaired -excludeRegions $mash_dark_region_hg38_bed -valueWigs methyPrior:0:$wgbs_buffycoat_hg38_bw -wgsMode &&\

Step 2: train the model

step2_max_memory="100G"

java -Xmx40G -cp "$FinaleMe/FinaleMe-0.58-jar-with-dependencies.jar:$FinaleMe/lib/jahmm-0.6.2.jar" \ org.cchmc.epifluidlab.finaleme.hmm.FinaleMe \ $outdir/$filename.FinaleMe.mincg7.model $outdir/CpgMultiMetricsStats.hg38.details.bed.gz \ $outdir/$filename.FinaleMe.mincg7.prediction.bed.gz -miniDataPoints 7 -gmm -covOutlier 3 &&\

Step 3: decode and make the prediction of CpG methylation level

step_3_max_memory="100G"

java -Xmx40G -cp "$FinaleMe/FinaleMe-0.58-jar-with-dependencies.jar:$FinaleMe/lib/jahmm-0.6.2.jar" \ org.cchmc.epifluidlab.finaleme.hmm.FinaleMe \ $outdir/$filename.FinaleMe.mincg7.model \ $outdir/CpgMultiMetricsStats.hg38.details.bed.gz \ $outdir/$filename.FinaleMe.mincg7.prediction.bed.gz -decodeModeOnly &&\