Estimation motifs #78
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HendrikSchultheis
requested changes
Jan 19, 2019
README.md
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| **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.
README.md
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| 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:
README.md
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| ``` | ||
| **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: | ||
| ``` | ||
| 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.
README.md
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| --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. (Needs absolute path) | ||
| or | ||
| --tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run. (Needs absolute path) |
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...will be skipped.
README.md
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| Moitf clustering: | ||
| --cluster_motif Boolean If 1 pipeline clusters motifs. If its 0 it does not. (Default: 0) | ||
| --cluster_motif Boolean If 1 pipeline clusters motifs. If its 0 it does not. (Defaul: 0) |
HendrikSchultheis
approved these changes
Jan 19, 2019
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