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Updated mitra urls to zenodo or cloud
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@panushri25
panushri25 authored Jul 6, 2024
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Expand Up @@ -81,14 +81,14 @@ chrombpnet pipeline \

#### Input Format

- `-ibam` or `-ifrag` or `-itag`: input file path with filtered reads in one of bam, fragment or tagalign formats. Example files for supported types - [bam](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/ENCSR868FGK_merged.bam), [fragment](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/example.fragments.tsv), [tagalign](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/example.tagAlign)
- `-ibam` or `-ifrag` or `-itag`: input file path with filtered reads in one of bam, fragment or tagalign formats. Example files for supported types - [bam](https://storage.googleapis.com/chrombpnet_data/input_files/ENCSR868FGK_merged.bam), [fragment](https://storage.googleapis.com/chrombpnet_data/input_files/example.fragments.tsv), [tagalign](https://storage.googleapis.com/chrombpnet_data/input_files/example.tagAlign)
- `-d`: assay type. The following types are supported - "ATAC" or "DNASE"
- `-g`: reference genome fasta file. Example file human reference - [hg38.fa](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/hg38.genome.fa)
- `-c`: chromosome and size tab separated file. Example file in human reference - [hg38.chrom.sizes](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/hg38.chrom.sizes)
- `-p`: Input peaks in narrowPeak file format, and must have 10 columns, with values minimally for chr, start, end and summit (10th column). Every region is centered at start + summit internally, across all regions. Example file with [ENCSR868FGK](https://www.encodeproject.org/experiments/ENCSR868FGK/) dataset - [peaks.bed](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/ENCSR868FGK_relaxed_peaks_no_blacklist.bed)
- `-n`: Input nonpeaks (background regions)in narrowPeak file format, and must have 10 columns, with values minimally for chr, start, end and summit (10th column). Every region is centered at start + summit internally, across all regions. Example file with [ENCSR868FGK](https://www.encodeproject.org/experiments/ENCSR868FGK/) dataset - [nonpeaks.bed](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/ENCSR868FGK_nonpeaks_no_blacklist.bed). More instructions on how to make your own nonpeak file can be found in the [Preprocessing](https://github.com/kundajelab/chrombpnet/wiki/Preprocessing#generate-non-peaks-background-regions) guide.
- `-fl`: json file showing split of chromosomes for train, test and valid. Example 5 fold jsons for human reference - [folds](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/folds/)
- `-b`: Bias model in `.h5` format. Bias models are generally transferable across assay types following similar protocol. Repository of pre-trained bias models for use [here](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/bias_models/). Instructions to train custom bias model below.
- `-g`: reference genome fasta file. Example file human reference - [hg38.fa](https://storage.googleapis.com/chrombpnet_data/input_files/hg38.genome.fa)
- `-c`: chromosome and size tab separated file. Example file in human reference - [hg38.chrom.sizes](https://storage.googleapis.com/chrombpnet_data/input_files/hg38.chrom.sizes)
- `-p`: Input peaks in narrowPeak file format, and must have 10 columns, with values minimally for chr, start, end and summit (10th column). Every region is centered at start + summit internally, across all regions. Example file with [ENCSR868FGK](https://www.encodeproject.org/experiments/ENCSR868FGK/) dataset - [peaks.bed](https://storage.googleapis.com/chrombpnet_data/input_files/ENCSR868FGK_relaxed_peaks_no_blacklist.bed)
- `-n`: Input nonpeaks (background regions)in narrowPeak file format, and must have 10 columns, with values minimally for chr, start, end and summit (10th column). Every region is centered at start + summit internally, across all regions. Example file with [ENCSR868FGK](https://www.encodeproject.org/experiments/ENCSR868FGK/) dataset - [nonpeaks.bed](https://storage.googleapis.com/chrombpnet_data/input_files/ENCSR868FGK_nonpeaks_no_blacklist.bed). More instructions on how to make your own nonpeak file can be found in the [Preprocessing](https://github.com/kundajelab/chrombpnet/wiki/Preprocessing#generate-non-peaks-background-regions) guide.
- `-fl`: json file showing split of chromosomes for train, test and valid. Example 5 fold jsons for human reference - [folds](https://zenodo.org/records/7443683/files/folds.zip?download=1)
- `-b`: Bias model in `.h5` format. Bias models are generally transferable across assay types following similar protocol. Repository of pre-trained bias models for use [here](https://zenodo.org/records/7443683/files/bias_models.zip?download=1). Instructions to train custom bias model below.
- `-o`: Output directory path

Please find scripts and best practices for preprocssing [here](https://github.com/kundajelab/chrombpnet/wiki/Preprocessing).
Expand Down Expand Up @@ -158,13 +158,13 @@ chrombpnet bias pipeline \

#### Input Format

- `-ibam` or `-ifrag` or `-itag`: input file path with filtered reads in one of bam, fragment or tagalign formats. Example files for supported types - [bam](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/ENCSR868FGK_merged.bam), [fragment](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/example.fragments.tsv), [tagalign](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/example.tagAlign)
- `-ibam` or `-ifrag` or `-itag`: input file path with filtered reads in one of bam, fragment or tagalign formats. Example files for supported types - [bam](https://storage.googleapis.com/chrombpnet_data/input_files/ENCSR868FGK_merged.bam), [fragment](https://storage.googleapis.com/chrombpnet_data/input_files/example.fragments.tsv), [tagalign](https://storage.googleapis.com/chrombpnet_data/input_files/example.tagAlign)
- `-d`: assay type. Following types are supported - "ATAC" or "DNASE"
- `-g`: reference genome fasta file. Example file human reference - [hg38.fa](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/hg38.genome.fa)
- `-c`: chromosome and size tab separated file. Example file in human reference - [hg38.chrom.sizes](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/hg38.chrom.sizes)
- `-p`: Input peaks in narrowPeak file format, and must have 10 columns, with values minimally for chr, start, end and summit (10th column). Every region is centered at start + summit internally, across all regions. Example file with [ENCSR868FGK](https://www.encodeproject.org/experiments/ENCSR868FGK/) dataset - [peaks.bed](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/ENCSR868FGK_relaxed_peaks_no_blacklist.bed)
- `-n`: Input nonpeaks (background regions)in narrowPeak file format, and must have 10 columns, with values minimally for chr, start, end and summit (10th column). Every region is centered at start + summit internally, across all regions. Example file with [ENCSR868FGK](https://www.encodeproject.org/experiments/ENCSR868FGK/) dataset - [nonpeaks.bed](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/ENCSR868FGK_nonpeaks_no_blacklist.bed)
- `-f`: json file showing split of chromosomes for train, test and valid. Example 5 fold jsons for human reference - [folds](https://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/folds/)
- `-g`: reference genome fasta file. Example file human reference - [hg38.fa](https://storage.googleapis.com/chrombpnet_data/input_files/hg38.genome.fa)
- `-c`: chromosome and size tab separated file. Example file in human reference - [hg38.chrom.sizes](https://storage.googleapis.com/chrombpnet_data/input_files/hg38.chrom.sizes)
- `-p`: Input peaks in narrowPeak file format, and must have 10 columns, with values minimally for chr, start, end and summit (10th column). Every region is centered at start + summit internally, across all regions. Example file with [ENCSR868FGK](https://www.encodeproject.org/experiments/ENCSR868FGK/) dataset - [peaks.bed](https://storage.googleapis.com/chrombpnet_data/input_files/ENCSR868FGK_relaxed_peaks_no_blacklist.bed)
- `-n`: Input nonpeaks (background regions)in narrowPeak file format, and must have 10 columns, with values minimally for chr, start, end and summit (10th column). Every region is centered at start + summit internally, across all regions. Example file with [ENCSR868FGK](https://www.encodeproject.org/experiments/ENCSR868FGK/) dataset - [nonpeaks.bed](https://storage.googleapis.com/chrombpnet_data/input_files/ENCSR868FGK_nonpeaks_no_blacklist.bed)
- `-f`: json file showing split of chromosomes for train, test and valid. Example 5 fold jsons for human reference - [folds](https://zenodo.org/records/7443683/files/folds.zip?download=1)
- `-o`: Output directory path

Please find scripts and best practices for preprocessing [here](https://github.com/kundajelab/chrombpnet/wiki/Preprocessing).
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