Update README.md #61

renewiegandt · 2019-01-12T09:49:55Z

No description provided.

…olab/masterJLU2018 into estimation_motifs

JannikHamp · 2019-01-12T11:39:39Z

Default von max bei motif_filtering bei mir ist 200, nicht 100. Hatte sich geändert.

JannikHamp · 2019-01-12T11:42:02Z

In the last code section, when you mention the rare moods bug, maybe add, that the pipeline (in step 1.2) checks if those files are empty and returns an error message if so. Or is this clear?

HendrikSchultheis · 2019-01-12T11:44:42Z

README.md

 this can be done with following commands:
 ```
 export PATH=[meme-suite instalation path]/libexec/meme-[meme-suite version]:$PATH
 export PATH=[meme-suite instalation path]/bin:$PATH
 ```

-Every other dependency will be automatically  installed by Nextflow using conda. For that a new conda enviroment will be created, which can be found in the from Nextflow created work directory after the first pipeline run.
-It is **not** required to create and activate the enviroment from the yaml-file beforehand.
+3. Every other dependency will be automatically  installed using conda. For that a conda enviroment has to be created from the yaml-file given in this repository.


Two whitespaces after 'automatically'.

HendrikSchultheis · 2019-01-12T11:50:52Z

README.md

 	Filter unknown motifs:
 	--min_size_fp INT	Minimum sequence length threshold. Smaller sequences are discarded. (Default: 10)
 	--max_size_fp INT	Maximum sequence length threshold. Discards all sequences longer than this value. (Default: 100)
-
+	--tfbsscan_method [moods|fimo] Method used by tfbsscan. (Default: moods)
 	Clustering:
 	Sequence preparation/ reduction:
 	--kmer INT		Kmer length (Default: 10)


*K-mer length

HendrikSchultheis · 2019-01-12T11:52:35Z

README.md

 	Clustering:
 	--global INT		Global (=1) or local (=0) alignment. (Default: 0)
 	--identity FLOAT	Identity threshold. (Default: 0.8)
 	--sequence_coverage INT	Minimum aligned nucleotides on both sequences. (Default: 8)
 	--memory INT		Memory limit in MB. 0 for unlimited. (Default: 800)
 	--throw_away_seq INT	Remove all sequences equal or below this length before clustering. (Default: 9)
 	--strand INT		Align +/+ & +/- (= 1). Or align only +/+ (= 0). (Default: 0)
-
 	Motif estimation:
 	--min_seq INT 		Sets the minimum number of sequences required for the FASTA-files given to GLAM2. (Default: 100)
 	--motif_min_key INT	Minimum number of key positions (aligned columns) in the alignment done by GLAM2. (Default: 8)
 	--motif_max_key INT	Maximum number of key positions (aligned columns) in the alignment done by GLAM2.f (Default: 20)


HendrikSchultheis · 2019-01-12T11:53:02Z

README.md

 	Clustering:
 	--global INT		Global (=1) or local (=0) alignment. (Default: 0)
 	--identity FLOAT	Identity threshold. (Default: 0.8)
 	--sequence_coverage INT	Minimum aligned nucleotides on both sequences. (Default: 8)
 	--memory INT		Memory limit in MB. 0 for unlimited. (Default: 800)
 	--throw_away_seq INT	Remove all sequences equal or below this length before clustering. (Default: 9)
 	--strand INT		Align +/+ & +/- (= 1). Or align only +/+ (= 0). (Default: 0)
-
 	Motif estimation:
 	--min_seq INT 		Sets the minimum number of sequences required for the FASTA-files given to GLAM2. (Default: 100)
 	--motif_min_key INT	Minimum number of key positions (aligned columns) in the alignment done by GLAM2. (Default: 8)
 	--motif_max_key INT	Maximum number of key positions (aligned columns) in the alignment done by GLAM2.f (Default: 20)
 	--iteration INT		Number of iterations done by glam2. More Iterations: better results, higher runtime. (Default: 10000)


Here is glam2 all lowercase before all uppercase.

HendrikSchultheis · 2019-01-12T11:54:57Z

README.md

-When the environment is created, set the variable 'path_env' in the configuration file as the path to it.
+
+For unknown reasons Moods, whisch is called by tfbsscan, rarely returns empty bedfiles. If this happens The pipeline stops.
+The is no known fix sofar. If it happens try starting the pipeline again. If it still fails. Change the parameter tfbsscan_method to 'fimo'. This methods takes longer but will cause no error.


*There is
*so far

As a workaround either restart the pipeline or change the parameter tfbsscan_method to fimo. (Instead of the third and second to last sentences).

renewiegandt · 2019-01-12T12:17:17Z

In the last code section, when you mention the rare moods bug, maybe add, that the pipeline (in step 1.2) checks if those files are empty and returns an error message if so. Or is this clear?

Can you give me the error message? then iI will add it

renewiegandt · 2019-01-12T12:24:06Z

The Parameter list is still not p to date. Please do not merge before it is.
I am going to update the list later this day.

JannikHamp · 2019-01-12T14:27:08Z

if [ $all_empty == true ]
then
echo ERROR
echo All motiffiles have less than 2 lines!
echo Fix motiffiles and try again.
exit 1
fi

SebastianBeyvers

We should reformat the Parameters page to one format.
And its called enviroNment with n :D

SebastianBeyvers · 2019-01-12T14:38:42Z

README.md

+3. Every other dependency will be automatically installed using conda. For that a conda enviroment has to be created from the yaml-file given in this repository.
+It is required to create and activate the enviroment from the yaml-file beforehand.
+This can be done with following commands:
+```condsole


SebastianBeyvers · 2019-01-12T14:43:29Z

README.md


 **Important Note:** For conda the channel bioconda needs to be set as highest priority! This is required due to two different packages with the same name in different channels. For the pipeline the package jellyfish from the channel bioconda is needed and **NOT** the jellyfish package from the channel conda-forge!


+
 ## Quick Start
 ```console
 nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file]


organism ?!

SebastianBeyvers · 2019-01-12T14:44:54Z

README.md

 Optional arguments:
-
 	--help [0|1]		1 to show this help message. (Default: 0)
 	--tfbs_path 		Path to directory with output from tfbsscan. If given tfbsscan will not be run.
 	--create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored.
 				 Path can be set as tfbs_path in next run. (Default: './')
 	--gtf_path			Path to gtf-file. If path is set the process which creats a gtf-file is skipped.


Arguments should be in one Format: With Datatype e.g. INT or without, not mixed within the document.

If its a list of strings which are allowed I prefer to write the list instead of 'STRING'. I could add 'STRING' to every path variable but I don't think that is necessary.

SebastianBeyvers · 2019-01-12T14:45:25Z

README.md

-	--motif_max_key INT	Maximum number of key positions (aligned columns) in the alignment done by GLAM2.f (Default: 20)
-	--iteration INT		Number of iterations done by glam2. More Iterations: better results, higher runtime. (Default: 10000)
+	--motif_max_key INT	Maximum number of key positions (aligned columns) in the alignment done by GLAM2. (Default: 20)
+	--iteration INT		Number of iterations done by GLAM2. More Iterations: better results, higher runtime. (Default: 10000)
 	--tomtom_treshold float	Threshold for similarity score. (Default: 0.01)


Datatypes all-caps or not -> only one format should be used

SebastianBeyvers · 2019-01-12T14:46:37Z

README.md

-Start with installing all dependencies listed above (Nextflow, conda, MEME-Suite) and downloading all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018).
-It is required to set the [enviroment paths for meme-suite](http://meme-suite.org/doc/install.html?man_type=web#installingtar).
+1. Start with installing all dependencies listed above (Nextflow, conda, MEME-Suite) and downloading all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018).
+2. It is required to set the [enviroment paths for meme-suite](http://meme-suite.org/doc/install.html?man_type=web#installingtar).


enviroNment not enviroment

SebastianBeyvers · 2019-01-12T14:46:56Z

README.md

 this can be done with following commands:
 ```
 export PATH=[meme-suite instalation path]/libexec/meme-[meme-suite version]:$PATH
 export PATH=[meme-suite instalation path]/bin:$PATH
 ```

-Every other dependency will be automatically  installed by Nextflow using conda. For that a new conda enviroment will be created, which can be found in the from Nextflow created work directory after the first pipeline run.
-It is **not** required to create and activate the enviroment from the yaml-file beforehand.
+3. Every other dependency will be automatically installed using conda. For that a conda enviroment has to be created from the yaml-file given in this repository.


enviroNment

SebastianBeyvers · 2019-01-12T14:47:23Z

README.md

-Every other dependency will be automatically  installed by Nextflow using conda. For that a new conda enviroment will be created, which can be found in the from Nextflow created work directory after the first pipeline run.
-It is **not** required to create and activate the enviroment from the yaml-file beforehand.
+3. Every other dependency will be automatically installed using conda. For that a conda enviroment has to be created from the yaml-file given in this repository.
+It is required to create and activate the enviroment from the yaml-file beforehand.


enviroNment

I think we needed the better explanation for the problem with MOODS

anastasiia

I added the better explanation for the issue with MOODS

anastasiia

here are the changes for the known issue with moods

…olab/masterJLU2018 into estimation_motifs

README.md

SebastianBeyvers

Looks fine (for now :D)

renewiegandt added 3 commits January 10, 2019 07:36

Merge branch 'dev' into estimation_motifs

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Merge branch 'estimation_motifs' of https://github.molgen.mpg.de/loos…

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…olab/masterJLU2018 into estimation_motifs

Update README.md

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renewiegandt requested review from HendrikSchultheis, anastasiia, JannikHamp and SebastianBeyvers January 12, 2019 09:49

Merge branch 'dev' into estimation_motifs

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HendrikSchultheis requested changes Jan 12, 2019

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pipeline.nf: Default of parameter max_size_fp is set to 200

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README.md: fixed typos

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Update README.md

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Update README.md

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I think we needed the better explanation for the problem with MOODS

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renewiegandt added 8 commits January 12, 2019 19:25

Update README.md

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Merge branch 'estimation_motifs' of https://github.molgen.mpg.de/loos…

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…olab/masterJLU2018 into estimation_motifs

yml: fixed version of python and numpy to prevent bug in 1.1

f371e1d

remove personal path from nextflow.config

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renamed config files

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Update README and help message in pipeline

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pipeline.nf: added missing params.

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Fixed typo

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Updated configs to new parameteres

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HendrikSchultheis approved these changes Jan 13, 2019

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renewiegandt added 2 commits January 13, 2019 07:39

Added demo run files

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Added demo command to README.md

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Added missing letter in README.md

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renewiegandt merged commit 9b849f2 into dev Jan 13, 2019

Update README.md #61

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