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Estimation motifs #78

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Jan 19, 2019
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Estimation motifs #78

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eab7672
README: Updated demo
renewiegandt Jan 18, 2019
ca5ff36
pipeline.nf: Update help message
renewiegandt Jan 18, 2019
c81a8d8
Merge branch 'dev' into estimation_motifs
renewiegandt Jan 18, 2019
00a5854
README: parameter update
renewiegandt Jan 18, 2019
47b4555
get_motif_seq.R: fixed bug mentioned in #77
renewiegandt Jan 18, 2019
da0f096
pipeline.nf: Added errorStrategy 'finish' to process createGTF; Minor…
renewiegandt Jan 18, 2019
4756f35
Added known tfbs sites for demo run
renewiegandt Jan 18, 2019
c1bfee4
README: Fixed typos
renewiegandt Jan 19, 2019
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README: Updated demo
@renewiegandt
renewiegandt committed Jan 18, 2019
commit eab76726102cf0481b01076c5c9464fa7078f332
14 changes: 10 additions & 4 deletions README.md
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@@ -29,21 +29,27 @@ conda activate masterenv
4. Set the wd parameter in the nextflow.config file as path where the repository is saved. For example: '~/masterJLU2018/'.


**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!

**Important Notes:**
1. 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!
2. The paramtere --create_known_tfbs_path and --tfbs_path need the absolute path. If a relative path is given it will not work due to nextflow changing the working directory. This will soon be updated.
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...need an absolute path.



## Quick Start
```console
nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --organism [mm10|mm9|hg19|hg38]
nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --organism [mm10|mm9|hg19|hg38] (--tfbs_path [absolute PATH] || --create_known_tfbs_path [absolute PATH])
```

### Demo run
There are files provided inside ./demo/ for a demo run.
Go to the main directory and run following command:
```
nextflow run pipeline.nf --bigwig ./demo/buenrostro50k_chr1_fp.bw --bed ./demo/buenrostro50k_chr1_peaks.bed --genome_fasta ./demo/hg38/hg38_chr1.fa --motif_db ./demo/motif_database/jaspar_vertebrates.meme --out ./demo/buenrostro50k_chr1_out/ --create_known_tfbs_path ./demo/known_tfbs_hg38_chr1/ --organism hg38
nextflow run pipeline.nf --bigwig ./demo/buenrostro50k_chr1_fp.bw --bed ./demo/buenrostro50k_chr1_peaks.bed --genome_fasta ./demo/hg38/hg38_chr1.fa --motif_db ./demo/motif_database/jaspar_vertebrates.meme --out ./demo/buenrostro50k_chr1_out/ --create_known_tfbs_path [absolute path]/demo/known_tfbs/ --organism hg38
```
**Important Note:** In can happen that tfbsscan does not work due to an unknown bug. If this is the case you will see the error message shown in "Known Issues". If this occurs and "fimo" will also throw this error, try following command:
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'It' not 'in'
...shown in the Known Issues section below.
If the error occurs first try to change the tfbsscan_method to fimo. If it persists try the following command:

```
nextflow run pipeline.nf --bigwig ./demo/buenrostro50k_chr1_fp.bw --bed ./demo/buenrostro50k_chr1_peaks.bed --genome_fasta ./demo/hg38/hg38_chr1.fa --motif_db ./demo/motif_database/jaspar_vertebrates.meme --out ./demo/buenrostro50k_chr1_out/ --tfbs_path [absolute path]/demo/known_tfbs_chr1_hg38/ --organism hg38
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Please verify that this and the nextflow call above are correct. To me it seems that you just changed the parameter create_known_tfbs_path to tfbs_path between the two.

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Oh I think I figured it out. The tfbs_scan provides already scanned data so tfbsscan can be skipped, right?

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Yes, that's correct. With the parameter tfbs_path, you can provide scanned data. So tfbsscan.py will be skipped.

```


## Parameters
For a detailed overview for all parameters follow this [link](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki/Configuration).