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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| wc -l /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/$2/$1/preds_upload/fold_0/$1_w_bias_all_regions.bed | ||
| zcat /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/$2/$1/merge_folds_all_regions_may_05_24/$1_folds_merged.profile_scores_new_compressed.bed.gz | wc -l | ||
| zcat /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/$2/$1/merge_folds_all_regions_may_05_24/$1_folds_merged.counts_scores_new_compressed.bed.gz | wc -l | ||
| bedtools sort -i /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/$2/$1/preds_upload/fold_0/$1_w_bias_all_regions.bed | uniq | wc -l | ||
| bedtools sort -i /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/$2/$1/merge_folds_all_regions_may_05_24/$1_folds_merged.counts_scores_new_compressed.bed.gz | zcat | cut -f1,2,3 | uniq | wc -l |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| oakdir="/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/DNASE/" | ||
| celltype="HEPG2" | ||
| zcat $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.bed" > $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" | ||
| wc -l $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" | ||
| python /mnt/lab_data2/anusri/chrombpnet/src/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py \ | ||
| -h5 $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.h5" \ | ||
| -r $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" \ | ||
| -c /mnt/lab_data2/anusri/chrombpnet/reference/chrom.sizes \ | ||
| -o $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores.bw" \ | ||
| -s $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores.stat" \ | ||
| -t 1 | ||
|
|
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| celltype="K562" | ||
| zcat $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.bed" > $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" | ||
| wc -l $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" | ||
| python /mnt/lab_data2/anusri/chrombpnet/src/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py \ | ||
| -h5 $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.h5" \ | ||
| -r $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" \ | ||
| -c /mnt/lab_data2/anusri/chrombpnet/reference/chrom.sizes \ | ||
| -o $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores.bw" \ | ||
| -s $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores.stat" \ | ||
| -t 1 | ||
|
|
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| celltype="GM12878" | ||
| zcat $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.bed" > $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" | ||
| wc -l $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" | ||
| python /mnt/lab_data2/anusri/chrombpnet/src/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py \ | ||
| -h5 $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.h5" \ | ||
| -r $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" \ | ||
| -c /mnt/lab_data2/anusri/chrombpnet/reference/chrom.sizes \ | ||
| -o $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores.bw" \ | ||
| -s $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores.stat" \ | ||
| -t 1 | ||
|
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| celltype="IMR90" | ||
| zcat $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.bed" > $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" | ||
| wc -l $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" | ||
| python /mnt/lab_data2/anusri/chrombpnet/src/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py \ | ||
| -h5 $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.h5" \ | ||
| -r $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" \ | ||
| -c /mnt/lab_data2/anusri/chrombpnet/reference/chrom.sizes \ | ||
| -o $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores.bw" \ | ||
| -s $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores.stat" \ | ||
| -t 1 | ||
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| celltype="H1ESC" | ||
| zcat $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.bed" > $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" | ||
| wc -l $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" | ||
| python /mnt/lab_data2/anusri/chrombpnet/src/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py \ | ||
| -h5 $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.h5" \ | ||
| -r $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores_new_compressed.unzip.bed" \ | ||
| -c /mnt/lab_data2/anusri/chrombpnet/reference/chrom.sizes \ | ||
| -o $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores.bw" \ | ||
| -s $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.counts_scores.stat" \ | ||
| -t 1 |
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logs/checkpoint/JAN_02_2023/dnase_make_average_bigwigs_profile.sh
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| oakdir="/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/DNASE/" | ||
| celltype="HEPG2" | ||
| zcat $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.bed" > $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" | ||
| wc -l $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" | ||
| python /mnt/lab_data2/anusri/chrombpnet/src/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py \ | ||
| -h5 $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.h5" \ | ||
| -r $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" \ | ||
| -c /mnt/lab_data2/anusri/chrombpnet/reference/chrom.sizes \ | ||
| -o $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores.bw" \ | ||
| -s $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores.stat" \ | ||
| -t 1 | ||
|
|
||
| celltype="K562" | ||
| zcat $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.bed" > $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" | ||
| wc -l $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" | ||
| python /mnt/lab_data2/anusri/chrombpnet/src/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py \ | ||
| -h5 $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.h5" \ | ||
| -r $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" \ | ||
| -c /mnt/lab_data2/anusri/chrombpnet/reference/chrom.sizes \ | ||
| -o $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores.bw" \ | ||
| -s $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores.stat" \ | ||
| -t 1 | ||
|
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||
| celltype="GM12878" | ||
| zcat $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.bed" > $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" | ||
| wc -l $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" | ||
| python /mnt/lab_data2/anusri/chrombpnet/src/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py \ | ||
| -h5 $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.h5" \ | ||
| -r $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" \ | ||
| -c /mnt/lab_data2/anusri/chrombpnet/reference/chrom.sizes \ | ||
| -o $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores.bw" \ | ||
| -s $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores.stat" \ | ||
| -t 1 | ||
|
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||
|
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| celltype="IMR90" | ||
| zcat $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.bed" > $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" | ||
| wc -l $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" | ||
| python /mnt/lab_data2/anusri/chrombpnet/src/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py \ | ||
| -h5 $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.h5" \ | ||
| -r $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" \ | ||
| -c /mnt/lab_data2/anusri/chrombpnet/reference/chrom.sizes \ | ||
| -o $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores.bw" \ | ||
| -s $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores.stat" \ | ||
| -t 1 | ||
|
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||
|
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| celltype="H1ESC" | ||
| zcat $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.bed" > $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" | ||
| wc -l $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" | ||
| python /mnt/lab_data2/anusri/chrombpnet/src/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py \ | ||
| -h5 $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.h5" \ | ||
| -r $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores_new_compressed.unzip.bed" \ | ||
| -c /mnt/lab_data2/anusri/chrombpnet/reference/chrom.sizes \ | ||
| -o $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores.bw" \ | ||
| -s $oakdir/$celltype/merge_folds_new/$celltype"_folds_merged.profile_scores.stat" \ | ||
| -t 1 |
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