!ngsplotdb.py list
ID Assembly Species EnsVer NPVer hg19 GRCh37 homo_sapiens 71.0 1.01 mm9 NCBIM37 mus_musculus 67.0 1.01 rn4 RGSC3.4 rattus_norvegicus 69.0 1.01
!ngsplotdb.py install /Users/steven/Downloads/ngsplotdb_GCA000297895_22_3.00.tar.gz
Extracting information from package... contains 12 tables.
Will install new genome GCA000297895: Ensembl=> v22.0; ngs.plot=> v3.0. Continue?(y/n): ^CTraceback (most recent call last):
File "/usr/local/bioinformatics/ngsplot/bin/ngsplotdb.py", line 551, in <module>
args.func(root_path, args)
File "/usr/local/bioinformatics/ngsplot/bin/ngsplotdb.py", line 291, in install
ans = raw_input("Continue?(y/n): ")
KeyboardInterrupt
ngsplotdb.py install ngsplotdb_hg19_71_2.0.tar.gz # Install reference genome from a package file.
ngsplotdb.py remove hg19 # Remove installed genome.
ngsplotdb.py remove --ftr enhancer hg19 # Remove enhancer installation from hg19.
!ngs.plot.r -G hg19 -R tss -C hesc.H3k4me3.rmdup.sort.bam -O hesc.H3k4me3.tss -T H3K4me3 -L 3000 -FL 300
Loading R libraries.....Done
Configuring variables...
Using database:
/usr/local/bioinformatics/ngsplot/database/hg19/hg19.ensembl.genebody.protein_coding.RData
Done
Analyze bam files and calculate coverageopen: No such file or directory
Error in FUN("hesc.H3k4me3.rmdup.sort.bam"[[1L]], ...) :
failed to open SAM/BAM file
file: 'hesc.H3k4me3.rmdup.sort.bam'
Calls: headerIndexBam ... indexBam -> sapply -> sapply -> lapply -> FUN -> .Call
Execution halted
!ngs.plot.r 2>&1|less
7=Unpaired argument and value.
Visit http://code.google.com/p/ngsplot/wiki/ProgramArguments101 for details
Version: 2.08
Usage: ngs.plot.r -G genome -R region -C [cov|config]file
-O name [Options]
## Mandatory parameters:
-G Genome name. Use ngsplotdb.py list to show available genomes.
-R Genomic regions to plot: tss, tes, genebody, exon, cgi, enhancer, dhs or bed
-C Indexed bam file or a configuration file for multiplot
-O Name for output: multiple files will be generated
## Optional parameters related to configuration file:
-E Gene list to subset regions OR bed file for custom region
-T Image title
## Important optional parameters:
-F Further information provided to select database table or plottype:
This is a string of description separated by comma.
E.g. protein_coding,K562,rnaseq(order of descriptors does not matter)
means coding genes in K562 cell line drawn in rnaseq mode.
-D Gene database: ensembl(default), refseq
)
:
Visit http://code.google.com/p/ngsplot/wiki/ProgramArguments101 for details
Version: 2.08
Usage: ngs.plot.r -G genome -R region -C [cov|config]file
-O name [Options]
## Mandatory parameters:
-G Genome name. Use ngsplotdb.py list to show available genomes.
-R Genomic regions to plot: tss, tes, genebody, exon, cgi, enhancer, dhs or bed
-C Indexed bam file or a configuration file for multiplot
-O Name for output: multiple files will be generated
## Optional parameters related to configuration file:
-E Gene list to subset regions OR bed file for custom region
-T Image title
## Important optional parameters:
-F Further information provided to select database table or plottype:
This is a string of description separated by comma.
E.g. protein_coding,K562,rnaseq(order of descriptors does not matter)
means coding genes in K562 cell line drawn in rnaseq mode.
-D Gene database: ensembl(default), refseq
-I Shall interval be larger than flanking in plot?(0 or 1, default=automatic)
-L Flanking region size
-N Flanking region factor(will override flanking size)
-S Randomly sample the regions for plot, must be:(0, 1]
-P #CPUs to use. Set 0(default) for auto detection
## Misc. parameters:
-GO Gene order algorithm used in heatmaps: total(default), hc, max,
prod, diff, pca and none(according to gene list supplied)
-AL Algorithm used to normalize coverage vectors: spline(default), bin
-CS Chunk size for loading genes in batch(default=100)
-FL Fragment length used to calculate physical coverage(default=150)
-MQ Mapping quality cutoff to filter reads(default=20)
-SE Shall standard errors be plotted?(0 or 1)
-RB The fraction of extreme values to be trimmed on both ends
default=0, 0.05 means 5% of extreme values will be trimmed
-RZ Remove all zero profiles in heatmaps(default=1). Set 0 to keep them.
-SC Color scale used to map values to colors in a heatmap.
local(default): base on each individual heatmap
region: base on all heatmaps belong to the same region
global: base on all heatmaps together
min_val,max_val: custom scale using a pair of numerics
-FC Flooding fraction:[0, 1), default=0.02
-FI Forbid image output if set to 1(default=0)
-MW Moving window width to smooth avg. profiles, must be integer
1=no(default); 3=slightly; 5=somewhat; 9=quite; 13=super.
-H Opacity of shaded area, suggested value:[0, 0.5]
default=0, i.e. no shading, just curves
File "<ipython-input-13-d75790595379>", line 1 Visit http://code.google.com/p/ngsplot/wiki/ProgramArguments101 for details ^ SyntaxError: invalid syntax
!ngs.plot.r -G GCA000297895 -R exon -C /Volumes/web/cnidarian/BiGoRNA_GTGTCTAC_1.sorted.bam -O dfredy
Loading R libraries.....Done Configuring variables... Using database: /usr/local/bioinformatics/ngsplot/database/GCA000297895/GCA000297895.ensembl.exon.canonical.protein_coding.RData Done Analyze bam files and calculate coverage.......Done Plotting figures...Done Saving results...Done Wrapping results up...Done All done. Cheers!
!ls
(White Space Conflict) PAG_2014.ipynb BSMAP2MK_workflow.ipynb README.md BSMAP2view_larvae.ipynb README_old.md BiGill_CpG_Ensembl.ipynb Roberts_cv.ipynb BiGill_Gene_Methylation.ipynb Ruphi_OA_RNAseq.ipynb BiGill_RNAseq.ipynb SS_datacheck.ipynb BiGill_Tran_Elements.ipynb TJGR_CpG_binding.ipynb BiGill_array.ipynb TJGR_CpG_islands.ipynb BiGill_bsmap_genometest.ipynb TJGR_Ensembl.ipynb BiGo - methratio error.ipynb TJGR_Methylation_GenomeSnapshot.ipynb BiGo_GFF_dev.ipynb TJGR_Mgo_Expression.ipynb BiGo_Larvae_QCC.ipynb TJGR_OysterGenome_IGV.ipynb BiGo_RNAseq.ipynb TJGR_ProteinAnnot.ipynb BiGo_SpermVSperm.ipynb TJGR_pearl.ipynb BiGo_larvae.ipynb Trait_Oo_exp.ipynb BiGo_larvae_2.ipynb UW_SoftwareBootcamp.ipynb BiGo_larvae_3.ipynb YE_DMR.ipynb BiGo_larvae_manuscript.ipynb _03_Widgets.ipynb BiGo_larvae_methylkit.ipynb _BiGO_expPLOT.ipynb BiGo_methratio.ipynb _BiGo_RNAseq.pdf BiGo_methratio_2.ipynb _BiGo_larvae_bsmap274.ipynb BiGo_methratio_mito.ipynb _IPsnapshot.ipynb BlackAb_Annot.ipynb _Larvae_Overrepresented_Sequences.ipynb CC_ampk.ipynb _scratch.ipynb ETS_ipig.ipynb bsmap2view_larvae_c.ipynb ETS_samifier.ipynb dfredy.avgprof.pdf ETS_samifier_2.ipynb dfredy.heatmap.pdf EY_methratio.ipynb dfredy.zip Gene Specific Methylation.ipynb examples Geoduck_hunt.ipynb fish546 LT_C1q.ipynb gen_workflows.ipynb MGarray_blast.ipynb hs_array.ipynb NGSplot.ipynb img OA_MS_data_check.ipynb intersectbed.ipynb OlyO_Chi_Exp.ipynb lft_v05_fasta2goslim.ipynb OlyO_GonadExp.ipynb meadow_log.ipynb OlyO_PacBio.ipynb qDOD_RNAseq2.ipynb OlyO_transcriptome.ipynb snippets.md OsHV_host.ipynb tools
cd /Volumes/web/cnidarian/
/Volumes/web/cnidarian
!ngs.plot.r -G GCA000297895 -R tss -C /Volumes/web/cnidarian/BiGoRNA_GTGTCTAC_1.sorted.bam -O ngsBiGoRNA
Loading R libraries.....Done Configuring variables... Using database: /usr/local/bioinformatics/ngsplot/database/GCA000297895/GCA000297895.ensembl.genebody.protein_coding.RData Done Analyze bam files and calculate coverage.Done Plotting figures...Done Saving results...Done Wrapping results up...Done All done. Cheers!
!ngs.plot.r -G GCA000297895 -R tes -C /Volumes/web/cnidarian/BiGoRNA_GTGTCTAC_1.sorted.bam -O ngs2BiGoRNA
Loading R libraries.....Done Configuring variables... Using database: /usr/local/bioinformatics/ngsplot/database/GCA000297895/GCA000297895.ensembl.genebody.protein_coding.RData Done Analyze bam files and calculate coverage.Done Plotting figures...Done Saving results...Done Wrapping results up...Done All done. Cheers!
!ngs.plot.r -G GCA000297895 -R exon -C /Volumes/web/cnidarian/BiGoRNA_GTGTCTAC_1.sorted.bam -O ngs3BiGoRNA
Loading R libraries.....Done Configuring variables... Using database: /usr/local/bioinformatics/ngsplot/database/GCA000297895/GCA000297895.ensembl.exon.canonical.protein_coding.RData Done Analyze bam files and calculate coverage.......Done Plotting figures...Done Saving results...Done Wrapping results up...Done All done. Cheers!
!ngs.plot.r -G GCA000297895 -R genebody -C /Volumes/web/cnidarian/BiGoRNA_GTGTCTAC_1.sorted.bam -O ngs4BiGoRNA
Loading R libraries.....Done Configuring variables... Using database: /usr/local/bioinformatics/ngsplot/database/GCA000297895/GCA000297895.ensembl.genebody.protein_coding.RData Done Analyze bam files and calculate coverage.Done Plotting figures...Done Saving results...Done Wrapping results up...Done All done. Cheers!
!ngs.plot.r -G GCA000297895 \
-R genebody \
-C /Volumes/web/cnidarian/BiGoRNA_GTGTCTAC_1.sorted.bam \
-O ngs4BiGoRNA
Loading R libraries.....Done Configuring variables... Using database: /usr/local/bioinformatics/ngsplot/database/GCA000297895/GCA000297895.ensembl.genebody.protein_coding.RData Done Analyze bam files and calculate coverage.Done Plotting figures...Done Saving results...Done Wrapping results up...Done All done. Cheers!
!ngs.plot.r -G GCA000297895 \
-R genebody \
-C //Volumes/web/cnidarian/SB_meth_sort.bam \
-O ngsP_SBmeth_gb_sort
Loading R libraries.....Done Configuring variables... Using database: /usr/local/bioinformatics/ngsplot/database/GCA000297895/GCA000297895.ensembl.genebody.protein_coding.RData Done Analyze bam files and calculate coverage.Done Plotting figures...Done Saving results...Done Wrapping results up...Done All done. Cheers!
!ngs.plot.r -G GCA000297895 \
-R exon \
-C /Volumes/web/cnidarian/SB_meth_mapping.bam:/Volumes/web/cnidarian/SB_UNmeth_mapping.bam \
-O ngsP_SBmeth_UNmeth_exon
Loading R libraries.....Done Configuring variables... Using database: /usr/local/bioinformatics/ngsplot/database/GCA000297895/GCA000297895.ensembl.exon.canonical.protein_coding.RData Done Analyze bam files and calculate coverage..............Done Plotting figures...Done Saving results...Done Wrapping results up...Done All done. Cheers!
!ngs.plot.r -G GCA000297895 \
-R tes \
-C /Volumes/web/cnidarian/SB_meth_mapping.bam \
-O ngsP_SBmeth_tes
Loading R libraries.....Done Configuring variables... Using database: /usr/local/bioinformatics/ngsplot/database/GCA000297895/GCA000297895.ensembl.genebody.protein_coding.RData Done Analyze bam files and calculate coverage.Done Plotting figures...Done Saving results...Done Wrapping results up...Done All done. Cheers!
!ngs.plot.r -G GCA000297895 \
-R tss \
-C /Volumes/web/cnidarian/SB_meth_mapping.bam \
-O ngsP_SBmeth_tss
Loading R libraries.....Done Configuring variables... Using database: /usr/local/bioinformatics/ngsplot/database/GCA000297895/GCA000297895.ensembl.genebody.protein_coding.RData Done Analyze bam files and calculate coverage.Done Plotting figures...Done Saving results...Done Wrapping results up...Done All done. Cheers!
cd /Volumes/web/cnidarian/
/Volumes/web/cnidarian
Unpaired argument and value.
Visit http://code.google.com/p/ngsplot/wiki/ProgramArguments101 for details
Version: 2.08
Usage: ngs.plot.r -G genome -R region -C [cov|config]file
-O name [Options]
## Mandatory parameters:
-G Genome name. Use ngsplotdb.py list to show available genomes.
-R Genomic regions to plot: tss, tes, genebody, exon, cgi, enhancer, dhs or bed
-C Indexed bam file or a configuration file for multiplot
-O Name for output: multiple files will be generated
## Optional parameters related to configuration file:
-E Gene list to subset regions OR bed file for custom region
-T Image title
## Important optional parameters:
-F Further information provided to select database table or plottype:
This is a string of description separated by comma.
E.g. protein_coding,K562,rnaseq(order of descriptors does not matter)
means coding genes in K562 cell line drawn in rnaseq mode.
-D Gene database: ensembl(default), refseq
-I Shall interval be larger than flanking in plot?(0 or 1, default=automatic)
-L Flanking region size
-N Flanking region factor(will override flanking size)
-S Randomly sample the regions for plot, must be:(0, 1]
-P #CPUs to use. Set 0(default) for auto detection
## Misc. parameters:
-GO Gene order algorithm used in heatmaps: total(default), hc, max,
prod, diff, pca and none(according to gene list supplied)
-AL Algorithm used to normalize coverage vectors: spline(default), bin
-CS Chunk size for loading genes in batch(default=100)
-FL Fragment length used to calculate physical coverage(default=150)
-MQ Mapping quality cutoff to filter reads(default=20)
-SE Shall standard errors be plotted?(0 or 1)
-RB The fraction of extreme values to be trimmed on both ends
default=0, 0.05 means 5% of extreme values will be trimmed
-RZ Remove all zero profiles in heatmaps(default=1). Set 0 to keep them.
-SC Color scale used to map values to colors in a heatmap.
local(default): base on each individual heatmap
region: base on all heatmaps belong to the same region
global: base on all heatmaps together
min_val,max_val: custom scale using a pair of numerics
-FC Flooding fraction:[0, 1), default=0.02
-FI Forbid image output if set to 1(default=0)
-MW Moving window width to smooth avg. profiles, must be integer
1=no(default); 3=slightly; 5=somewhat; 9=quite; 13=super.
-H Opacity of shaded area, suggested value:[0, 0.5]
default=0, i.e. no shading, just curves
Error: Error in parsing command line arguments. Stop.
Execution halted