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chipseq_pipeline's Issues
bug in calculate cc
jsd turned off for step1 (final_stage - xcor)
generate pileup track
runSE.pbs seems create `finished` tag for treat libs even it just finish step 1
add bin size in jsd to increase speed
bug exists in estimate dup reads number
bottleneck in bwa_sam_PE
taking long time to generate: /home/zhc268/scratch/outputs/AVD_146/align/rep1/AVD_146_R1.PE2SE.bam
for 1g size fastq.gz.
bwa sampe /projects/ps-epigen/GENOME/hg38/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta /home/zhc268/scratch/outputs/AVD_146/align/rep1/AVD_146_R1.sai /home/zhc268/scratch/outputs/AVD_146/align/rep1/AVD_146_R2.sai /home/zhc268/data/seqdata/AVD_146_R1.fastq.gz /home/zhc268/data/seqdata/AVD_146_R2.fastq.gz | pigz -p 5 -nc > /home/zhc268/scratch/outputs/AVD_146/align/rep1/AVD_146_R1.PE2SE.sam.gz
no data output for jsd curve
no tss enrichment
pdf_to_png for ctl's cc plot
no cc for ctl
two CC for 2step method
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cc calculated in both step 1 and step2
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Step1 is use R1-fastq and step2 is from "subsample_tag_PE_4_xcor"
alignment log/stat need update in chipqc
now use bwa not bowties.
seems not start from break point when 2nd run whole experiment
bwa_sam_PE error when request 32 cpu -P
cpus: 21 mem: -1.0 B wall-timeout: 8640000
need include screen & result transfer for ctl run in pbs file
repeated calculation of ctl when run set for jsd
fix jsd output dir
ctl's track
step 2's report overwrite step 1's
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