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Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

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Q:
I am reading your paper “Supervised enhancer prediction with epigenetic pattern recognition and targeted validation”, and I would greatly appreciate if you could provide some results apparently missing in Figure 2.

I am interested in the AUPR comparison of the matched-filter results with the peak-calling results, but I could not find the "gray" numbers.

Fig. 2 a, ….the gray numbers in the parentheses refer to the performance of the peak-based models.

A:
Thank you for bringing this to our attention and apologies for any confusion. We lost the numbers during one of the revisions. I am attaching a SI figure from an older version of the manuscript that answers your question.

In the table, I have compared the AUROC and AUPR for accuracy of different matched filter models (outside parentheses) with the corresponding peak based accuracy measures (within parentheses) for same histone marks. In this particular case, the comparison is made based on overlap with a single STARR-seq experiment but the trends remain the same even after combining information from multiple STARR-seq experiments within the same cell-line.

Trying to execute Pseudopipe but I am running into multiple errors

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Q1:
I am trying to execute Pseudopipe but I am running into multiple errors. I have downloaded the latest version from the website and the command I am using to run it is

/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/pseudopipe/bin/pseudopipe.sh /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_output/caenorhabditis_elegans_62_220a /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/Caenorhabditis_elegans.WS220.62.dna.chromosome.%s.fa /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/pep/Caenorhabditis_elegans.WS220.62.pep.fa /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/mysql/chrI_exLocs 0

I keep getting the following errors:

Making directories
Copying sequences
Fomatting the DNAs
/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/pseudopipe/bin/pseudopipe.sh: line 84: /home/bp272/bin/blast-2.2.13/bin/formatdb: No such file or directory
Preparing the blast jobs
Skipping blast
Processing blast output
/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/pseudopipe/bin/pseudopipe.sh: line 114: /home/bp272/bin/Python-2.6.6/python: No such file or directory
Finished processing blast output
Running Pseudopipe on both strands
Working on M strand
/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/pseudopipe/bin/pseudopipe.sh: line 144: /home/bp272/bin/Python-2.6.6/python: No such file or directory
Finished Pseudopipe on strand M
Working on P strand
/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/pseudopipe/bin/pseudopipe.sh: line 144: /home/bp272/bin/Python-2.6.6/python: No such file or directory
Finished Pseudopipe on strand P
Generating final results
find: ‘/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/minus/pgenes’: No such file or directory
find: ‘/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/plus/pgenes’: No such file or directory
gzip: /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/*/pgenes/*.all.fa: No such file or directory
Finished generating pgene full alignment
Finished running Pseudopipe

I am running this inside conda environment. I tried executing it outside but it gave me the same errors. Could you please help?

I have posted on the website under the comments section by mistake. Please excuse my ignorance.

A1:
It seems that you did not set the environment file (env.sh) correctly. You may need to set the it as the following and put in the same dir as fetchEnsemblFiles.py & processEnsemblFiles.sh

###
#!/bin/sh
if [ ! -z "$PSEUDOPIPE_ENV" ]; then source $PSEUDOPIPE_ENV; return; fi

# Pseudopipe configuration

export PSEUDOPIPE_HOME=`cd \`dirname $0\`/../; pwd`

export pseudopipe=$PSEUDOPIPE_HOME/core/runScripts.py

export genPgeneResult=$PSEUDOPIPE_HOME/ext/genPgeneResult.sh

export genFullAln=$PSEUDOPIPE_HOME/ext/genFullAln.sh

export fastaSplitter=$PSEUDOPIPE_HOME/ext/splitFasta.py

export sqDedicated=$PSEUDOPIPE_HOME/ext/sqDedicated.py

export sqDummy=$PSEUDOPIPE_HOME/ext/sqDummy.py

export blastHandler=$PSEUDOPIPE_HOME/core/processBlastOutput.py

export extractExLoc=$PSEUDOPIPE_HOME/core/extractKPExonLocations-Aug2016.py # extractKPExonLocations-Jan2016.py

# Python configuration

export pythonExec=/bin/python2

# Alignment tools configuration

export formatDB=/ysm-gpfs/pi/gerstein/yy532/software/blast-2.2.13/bin/formatdb

export blastExec=/ysm-gpfs/pi/gerstein/yy532/software/blast-2.2.13/bin/blastall

export fastaExec=/ysm-gpfs/pi/gerstein/yy532/software/fasta-35.1.5/tfasty35

Q2:
Thank you for your reply. I am using python3 in my pipeline. Will this code work for python3?

A2:
Please use python2.