slzhao
commented
9 years ago Hello Koen,
Is there any exonDelsBy1.csv or exonDelsCutoffs.csv file? You mentioned some of the samples have CNV, what is the content for the CNV regions in your ".bed.depth.all", ".bed.depth.all.adjustGC" files?
Best, Shilin
2015-07-27 7:05 GMT-05:00 Koen Hendriks notifications@github.com:
Hi Shilin,
I've managed to run ExonDel without errors. It finishes without giving any errors.
The console output can be seen hereunder:
[Mon Jul 27 10:55:47 2015] All genes will be used [Mon Jul 27 10:55:47 2015] Loading BED file [Mon Jul 27 10:55:47 2015] Finish BED file (cover 21634 base pairs) [Mon Jul 27 10:55:47 2015] Loading RefSeq file [Mon Jul 27 10:55:51 2015] Finish RefSeq file [Mon Jul 27 10:55:51 2015] Loading fasta file and caculating GC content [Mon Jul 27 10:56:10 2015] Caculating GC content in 13: 27 exons [Mon Jul 27 10:56:13 2015] Caculating GC content in 17: 136 exons [Mon Jul 27 10:56:18 2015] Finish fasta file [Mon Jul 27 10:56:18 2015] Loading genesPassQCwithGC.bed [Mon Jul 27 10:56:18 2015] Processing bam files [Mon Jul 27 10:56:18 2015] Thread 1 stared [Mon Jul 27 10:56:18 2015] Thread 1 processing /home/koen/new_BRCA_runs/150710_NS500265_0100_AH3LL2AFXX/DNA04-04209_BRCA1_R15-12598_B8_17151464.bam DNA04-04209_BRCA1_R15-12598_B8_171514 64 [Mon Jul 27 10:56:18 2015] Thread 2 stared [Mon Jul 27 10:56:18 2015] Thread 2 processing /home/koen/new_BRCA_runs/150710_NS500265_0100_AH3LL2AFXX/DNA04-04209_BRCA1_R15-12598_E7_17151463.bam DNA04-04209_BRCA1_R15-12598_E7_171514 63
etc. etc.
It then finishes with:
[Mon Jul 27 10:57:54 2015] Thread 1 finished [Mon Jul 27 10:58:04 2015] Thread 2 finished [Mon Jul 27 10:58:04 2015] Thread 3 finished [Mon Jul 27 10:58:04 2015] Thread 4 finished [Mon Jul 27 10:58:04 2015] Thread 5 finished [Mon Jul 27 10:58:04 2015] Thread 6 finished [Mon Jul 27 10:58:15 2015] Thread 7 finished [Mon Jul 27 10:58:15 2015] Thread 8 finished [Mon Jul 27 10:58:15 2015] Thread 9 finished [Mon Jul 27 10:58:15 2015] Thread 10 finished [Mon Jul 27 10:58:15 2015] Thread 11 finished [Mon Jul 27 10:58:15 2015] Thread 12 finished [Mon Jul 27 10:58:15 2015] Thread 13 finished [Mon Jul 27 10:58:15 2015] Thread 14 finished [Mon Jul 27 10:58:15 2015] Thread 15 finished [Mon Jul 27 10:58:15 2015] Finish bam file [Mon Jul 27 10:58:15 2015] Analyzing Exon Deletion [Mon Jul 27 10:58:17 2015] Success!
My config file contains;
config file for ExonDel software
[perl]
reference .bed file
bedfile=/home/koen/cnv_tool_comparison/reference_files/BRCA_1_2_new_mip_panel_sorted_merged_only_normal_mips.bed
reference .gtf file
refseq=/home/koen/cnv_tool_comparison/reference_files/refGene.hg19.24feb2015ucsc.gtf
reference .fa file
reffa=/data/references/hg19/ref_hg19.fasta
Minimal percent of covered base pairs for each exon
exon_bp_cover_threshold=0.1
Minimal percent of covered exons for each gene. 1 means 100%
overall_exon_count_threshold=0.001
Minimum mapping quality for an alignment to be used
mapQ=20
Minimum base quality for a base to be considered
baseQ=20
where the R bin file is
RBin=R
where the SAMtools bin file is
samtoolsBin=samtools
name of the log file
logFileName=ExonDel.log [R]
Maximal number of exons for the moving-window in exon deletion detection
maxWinLength=23
Minimum number of exons for the moving-window in exon deletion detection
minWinLength=1
Minimum number of exons for a gene to be considered in exon deletion
detection minExonNum=1
T means True and F means False. If only some genes were used (use -g
option), GC adjustment will not be performed no matter what adjustGC below was set (As GC adjustment is based on all ge nes). adjustGC=T
If all genes were used (didn't use -g option), cutoff 1,2 will be
determined by cutoffQuantile 1,2 in all genes cutoffQuantile1=0.01 cutoffQuantile2=0.1
If only some genes were used (use -g option), cutoff 1,2 will be
determined by constant cutoff 1,2 below cutoff1=2 cutoff2=20
All files, covered_percentage, genespassqc.bed(.bed.depth.all, .bed.depth.all.adjustGC), they're all there.
The only thing is that ExonDel doesn't call any CNV's, i.e. there are no figures being created and the results in the html report are empty.Some of my samples do have a CNV, so they should be called.
I hope to hear from you soon!
Best,
Koen
— Reply to this email directly or view it on GitHub https://github.com/slzhao/ExonDel/issues/7.
pineapple216
Hi Shilin,
I've managed to run ExonDel without errors. It finishes without giving any errors.
The console output can be seen hereunder:
[Mon Jul 27 10:55:47 2015] All genes will be used [Mon Jul 27 10:55:47 2015] Loading BED file [Mon Jul 27 10:55:47 2015] Finish BED file (cover 21634 base pairs) [Mon Jul 27 10:55:47 2015] Loading RefSeq file [Mon Jul 27 10:55:51 2015] Finish RefSeq file [Mon Jul 27 10:55:51 2015] Loading fasta file and caculating GC content [Mon Jul 27 10:56:10 2015] Caculating GC content in 13: 27 exons [Mon Jul 27 10:56:13 2015] Caculating GC content in 17: 136 exons [Mon Jul 27 10:56:18 2015] Finish fasta file [Mon Jul 27 10:56:18 2015] Loading genesPassQCwithGC.bed [Mon Jul 27 10:56:18 2015] Processing bam files [Mon Jul 27 10:56:18 2015] Thread 1 stared [Mon Jul 27 10:56:18 2015] Thread 1 processing /home/koen/new_BRCA_runs/150710_NS500265_0100_AH3LL2AFXX/DNA04-04209_BRCA1_R15-12598_B8_17151464.bam DNA04-04209_BRCA1_R15-12598_B8_171514 64 [Mon Jul 27 10:56:18 2015] Thread 2 stared [Mon Jul 27 10:56:18 2015] Thread 2 processing /home/koen/new_BRCA_runs/150710_NS500265_0100_AH3LL2AFXX/DNA04-04209_BRCA1_R15-12598_E7_17151463.bam DNA04-04209_BRCA1_R15-12598_E7_171514 63
etc. etc.
It then finishes with:
[Mon Jul 27 10:57:54 2015] Thread 1 finished [Mon Jul 27 10:58:04 2015] Thread 2 finished [Mon Jul 27 10:58:04 2015] Thread 3 finished [Mon Jul 27 10:58:04 2015] Thread 4 finished [Mon Jul 27 10:58:04 2015] Thread 5 finished [Mon Jul 27 10:58:04 2015] Thread 6 finished [Mon Jul 27 10:58:15 2015] Thread 7 finished [Mon Jul 27 10:58:15 2015] Thread 8 finished [Mon Jul 27 10:58:15 2015] Thread 9 finished [Mon Jul 27 10:58:15 2015] Thread 10 finished [Mon Jul 27 10:58:15 2015] Thread 11 finished [Mon Jul 27 10:58:15 2015] Thread 12 finished [Mon Jul 27 10:58:15 2015] Thread 13 finished [Mon Jul 27 10:58:15 2015] Thread 14 finished [Mon Jul 27 10:58:15 2015] Thread 15 finished [Mon Jul 27 10:58:15 2015] Finish bam file [Mon Jul 27 10:58:15 2015] Analyzing Exon Deletion [Mon Jul 27 10:58:17 2015] Success!
My config file contains;
config file for ExonDel software
[perl]
reference .bed file
bedfile=/home/koen/cnv_tool_comparison/reference_files/BRCA_1_2_new_mip_panel_sorted_merged_only_normal_mips.bed
reference .gtf file
refseq=/home/koen/cnv_tool_comparison/reference_files/refGene.hg19.24feb2015ucsc.gtf
reference .fa file
reffa=/data/references/hg19/ref_hg19.fasta
Minimal percent of covered base pairs for each exon
exon_bp_cover_threshold=0.1
Minimal percent of covered exons for each gene. 1 means 100%
overall_exon_count_threshold=0.001
Minimum mapping quality for an alignment to be used
mapQ=20
Minimum base quality for a base to be considered
baseQ=20
where the R bin file is
RBin=R
where the SAMtools bin file is
samtoolsBin=samtools
name of the log file
logFileName=ExonDel.log [R]
Maximal number of exons for the moving-window in exon deletion detection
maxWinLength=23
Minimum number of exons for the moving-window in exon deletion detection
minWinLength=1
Minimum number of exons for a gene to be considered in exon deletion detection
minExonNum=1
T means True and F means False. If only some genes were used (use -g option), GC adjustment will not be performed no matter what adjustGC below was set (As GC adjustment is based on all ge
nes). adjustGC=T
If all genes were used (didn't use -g option), cutoff 1,2 will be determined by cutoffQuantile 1,2 in all genes
cutoffQuantile1=0.01 cutoffQuantile2=0.1
If only some genes were used (use -g option), cutoff 1,2 will be determined by constant cutoff 1,2 below
cutoff1=2 cutoff2=20
All files, covered_percentage, genespassqc.bed(.bed.depth.all, .bed.depth.all.adjustGC), they're all there.
The only thing is that ExonDel doesn't call any CNV's, i.e. there are no figures being created and the results in the html report are empty.Some of my samples do have a CNV, so they should be called.
I hope to hear from you soon!
Best,
Koen