Beluga allows 2k sequence window

docs/deepsea.rst

@@ -11,7 +11,7 @@ The current version of DeepSEA, nicknamed '**Beluga**', can predict **2002** chr
 
 Jian Zhou, Chandra L. Theesfeld, Kevin Yao, Kathleen M. Chen, Aaron K. Wong, and Olga G. Troyanskaya, **Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk**. Nature Genetics (2018).
 
-DeepSEA is described in the following manuscript:
+DeepSEA is originally described in the following manuscript:
 
 Jian Zhou, Olga G. Troyanskaya. **Predicting the Effects of Noncoding Variants with Deep learning-based Sequence Model.** Nature Methods (2015).
 
@@ -20,33 +20,59 @@ To determine if certain features (ie. transcription factors, marks, or cell type
 Input
 -----
 
-DeepSEA predicts genomic variant effects on a wide range of chromatin features at the variant position (Transcription factors binding, DNase I hypersensitive sites, and histone marks in multiple human cell types). DeepSEA can also be ultilized for predicting chromatin features for any DNA sequence.
+DeepSEA predicts genomic variant effects on a wide range of chromatin features at the variant position (Transcription factors binding, DNase I hypersensitive sites, and histone marks in multiple human cell types). DeepSEA can also be utilized for predicting chromatin features for any DNA sequence.
 
 File formats
 ~~~~~~~~~~~~
 We support three types of input: vcf, fasta, bed. If you want to predict effects of noncoding variants, use vcf format input. If you want to predict chromatin feature probabilities for DNA sequences, use fasta format. If you want to specify sequences from the human reference genome (GRCh37/hg19), you can use bed format. See below for a quick introduction:
 
 **VCF format** is used for specifying a genomic variant. A minimal example is ``chr1 109817590 - G T`` (if you want to copy cover this text as input, you will need to change spaces to tabs). The five columns are chromosome, position, name, reference allele, and alternative allele.
 
-**Fasta format** input should include sequences of 1000bp length each. If a sequence is longer than 1000bp, only the center 1000bp will be used. A minimal example is ::
+**Fasta format** input should include sequences of 2000bp length each. If a sequence is longer than 2000bp, only the center 2000bp will be used. A minimal example is ::
 
   >TestSequence
-  TATCTCTCATGTTTCTGGTATAGATGGTATATATGTTAATCTTGTTCCTGAGGTCTGTTTTTTATTTTTGTCATTAAAGT
-  GGGAATTAAATAGTTTTGTAGTGCATATAAATTAAAGAAAAAGTTCACATAAGCATATTTGCCAATCATCTCAAAATGCT
-  ATATTCTCCTTCACGGTTTTGAAAATAATTCAGGGTTTTCTCTTCCTCATTGCTTTCCCACCAACTGACAGTATTATTTT
-  CTTAGTCATTTTACTGACCTTTGAAATTACTCCTTTGAGGTCTTCTAAAAAATTTTATGGGCTCTGCTGCTTTTTGGTGG
-  CCTCCTTGTATCATTTATTCTATTACAGGACGACTTACAAAAGGAAGCACATAAATTGACCCATATACATATCCTATCAT
-  TGGGGAGTTTCTGTGCAAATGTTATTTATTGGAAGCTATTACTAAGAATTGTAAGAAAAATAATTGGTATTGATGCAGCT
-  AGTATGGTTCCTGTAATTATCGTACTCAGCCACGTAAATCATAGCTATATGTAGCCAAAGATCCATGAACAAAATTTCCA
-  GTAACATCATTATAATTCAAAAGGCAGACTTTCAGAACCAGACAGACTTGAATTTAAATTCTAGCTTTACCACACATGAA
-  TTTAACCTTGTGGAAGGTTAACCTATCTAAACTCATGTTTCTTCATTGGTAGCTGATAAAATTAAGGATCATGTATATAA
-  CCACCTAGTAGAGTTGTTTAAGAAACTGTTAGAATTCCATAAATTGTTAGTATTAATGAGTTTTTGTTGGACATGTGTTA
-  GGCTAGGCCACTCCTTGACCTTCATAGAGGTATGGATTATGACACAAATTCTAAACTGTAGGTAGGCATGGCTTTGTAGC
-  AAGTATTAAAATAGTAAATATTTTATTTTTATAAGATAAATGTAAACCTTTTAAAAGTTTCATTACATTTGTATTTATGA
-  AATATCATCCTATATCAACTATAGAGAGAAGATCGCAAGA
-
-
-**Bed format** provides another way to specify sequences in human reference genome (hg19). The bed input should specify 1000bp-length regions. A minimal example is ``chr1 109817091 109818090``. The three columns are chromosome, start position, and end position.
+  TGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATTGTACCATTCTTAT
+  GCCTTTGCGTCCTCATAGCTTAGCTCCCGTATATCAGTGAGAACATACTA
+  TGTTTGGTTTTCCATACCCGAGTTACTTCACTTAGAATAATAGTCTCCAA
+  TTTCATCCAGGTCAGTGCAAATGCGTTAATTCGTTCCTTTTATGGCTGAG
+  TAGTATTCCATCATATATATATACTACAGTTTCTTTATCCACTCGTAAAT
+  TGATGGGCATTTGTGTTGGAACACTTCTCCACTGCTGGTGGGAATGTAAA
+  TTAGTGCAGCCACTATGGATAACAGTGTGGAGATTTGTTAAAGAACTAAA
+  ACTAGAACTACCATTTGATCCAGCAATCCCACTACTGGGTATCTACCCAG
+  AAGAAAAGAAGTCATTATTTGAAAAAGATACTTGCACGGGCATGTTTATA
+  GCAGCACAATTCACAATTGTAGTTGTATTTCTTTAAGCGTGTCTTTTCAA
+  TATCTCTCATGTTTCTGGTATAGATGGTATATATGTTAATCTTGTTCCTG
+  AGGTCTGTTTTTTATTTTTGTCATTAAAGTGGGAATTAAATAGTTTTGTA
+  GTGCATATAAATTAAAGAAAAAGTTCACATAAGCATATTTGCCAATCATC
+  TCAAAATGCTATATTCTCCTTCACGGTTTTGAAAATAATTCAGGGTTTTC
+  TCTTCCTCATTGCTTTCCCACCAACTGACAGTATTATTTTCTTAGTCATT
+  TTACTGACCTTTGAAATTACTCCTTTGAGGTCTTCTAAAAAATTTTATGG
+  GCTCTGCTGCTTTTTGGTGGCCTCCTTGTATCATTTATTCTATTACAGGA
+  CGACTTACAAAAGGAAGCACATAAATTGACCCATATACATATCCTATCAT
+  TGGGGAGTTTCTGTGCAAATGTTATTTATTGGAAGCTATTACTAAGAATT
+  GTAAGAAAAATAATTGGTATTGATGCAGCTAGTATGGTTCCTGTAATTAT
+  CGTACTCAGCCACGTAAATCATAGCTATATGTAGCCAAAGATCCATGAAC
+  AAAATTTCCAGTAACATCATTATAATTCAAAAGGCAGACTTTCAGAACCA
+  GACAGACTTGAATTTAAATTCTAGCTTTACCACACATGAATTTAACCTTG
+  TGGAAGGTTAACCTATCTAAACTCATGTTTCTTCATTGGTAGCTGATAAA
+  ATTAAGGATCATGTATATAACCACCTAGTAGAGTTGTTTAAGAAACTGTT
+  AGAATTCCATAAATTGTTAGTATTAATGAGTTTTTGTTGGACATGTGTTA
+  GGCTAGGCCACTCCTTGACCTTCATAGAGGTATGGATTATGACACAAATT
+  CTAAACTGTAGGTAGGCATGGCTTTGTAGCAAGTATTAAAATAGTAAATA
+  TTTTATTTTTATAAGATAAATGTAAACCTTTTAAAAGTTTCATTACATTT
+  GTATTTATGAAATATCATCCTATATCAACTATAGAGAGAAGATCGCAAGA
+  AGGCAGTGGCAGCAGAGGCTCCAGTTAGGAGGCTACTAGTCCAAATACAT
+  TGCGATAAAAACTTGGCAAAAGGTGCTGGTAGTCTGATGAAATAAAGTAG
+  ATAAATTTTAGAGGTATTTATAAAATAATTAAAGAATATTCAATAATAGG
+  AGATATATTACCCAATAGAGTGGAGATTCAAAGATAACTCCGAAAGTTTT
+  TTGCTAAAGCAACATTTGGCTGTGCTATCATTTACTAAGAAAGACAACAA
+  GAGAGTAAAATCAAGTTTGAGGATGAAGTGAATTTATTCCTTTTTGATTG
+  ATACATAATTGACATGTAATAAAACCCACAATGTTAAGAGTTCGGTTTGA
+  TGTGCTTGACTATTTTAGGCACTGGTGTTATCACAACACAAGACAACAGA
+  TAGGACATTCTCAGAAAATTTTTTCATGTCCCTTTCCAGTCAGTTTCAAG
+  CCTTCTTTCCATGCAATAATTTTCTCACTTTGCCATTCTAGTAGGTGTGA
+
+**Bed format** provides another way to specify sequences in human reference genome (hg19). The bed input should specify 2000bp-length regions. A minimal example is ``chr1 109817091 109819090``. The three columns are chromosome, start position, and end position.
 
 Genome coordinates
 ~~~~~~~~~~~~~~~~~~
@@ -85,4 +111,4 @@ Perform "In silico saturated mutagenesis" (ISM) analysis to discover informative
 
 Note that ISM only accepts a sequence (FASTA file) as input.
 
-ISM outputs effects for each of three possible substitutions of all 1000 bases, across all chromatin features.
+ISM outputs effects for each of three possible substitutions of all 2000 bases, across all chromatin features.