From d3684388512ad2248ac1c2d1dfd36167b634e816 Mon Sep 17 00:00:00 2001 From: Anusri Pampari Date: Tue, 25 Jul 2023 11:15:34 -0700 Subject: [PATCH] fixed links with the new address fixed links with the new address --- README.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index ff6a9f7b..832c4951 100644 --- a/README.md +++ b/README.md @@ -79,14 +79,14 @@ 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/akundaje/anusri/chrombpnet_data/input_files/ENCSR868FGK_merged.bam), [fragment](https://mitra.stanford.edu/kundaje/oak/akundaje/anusri/chrombpnet_data/input_files/example.fragments.tsv), [tagalign](https://mitra.stanford.edu/kundaje/oak/akundaje/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://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) - `-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/akundaje/anusri/chrombpnet_data/input_files/hg38.genome.fa) -- `-c`: chromosome and size tab seperated file. Example file in human reference - [hg38.chrom.sizes](https://mitra.stanford.edu/kundaje/oak/akundaje/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/akundaje/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/akundaje/anusri/chrombpnet_data/input_files/ENCSR868FGK_nonpeaks_no_blacklist.bed) -- `-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/akundaje/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/akundaje/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://mitra.stanford.edu/kundaje/oak/anusri/chrombpnet_data/input_files/hg38.genome.fa) +- `-c`: chromosome and size tab seperated 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) +- `-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. - `-o`: Output directory path Please find scripts and best practices for preprocssing [here](https://github.com/kundajelab/chrombpnet/wiki/Preprocessing). @@ -156,13 +156,13 @@ 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/akundaje/anusri/chrombpnet_data/input_files/ENCSR868FGK_merged.bam), [fragment](https://mitra.stanford.edu/kundaje/oak/akundaje/anusri/chrombpnet_data/input_files/example.fragments.tsv), [tagalign](https://mitra.stanford.edu/kundaje/oak/akundaje/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://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) - `-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/akundaje/anusri/chrombpnet_data/input_files/hg38.genome.fa) -- `-c`: chromosome and size tab seperated file. Example file in human reference - [hg38.chrom.sizes](https://mitra.stanford.edu/kundaje/oak/akundaje/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/akundaje/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/akundaje/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/akundaje/anusri/chrombpnet_data/input_files/folds/) +- `-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 seperated 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/) - `-o`: Output directory path Please find scripts and best practices for preprocssing [here](https://github.com/kundajelab/chrombpnet/wiki/Preprocessing).