Downloading data from ENCODE
Hi Everyone,
I want to download the data of Long Non-coding RNAs (lncRNAs) and I explored ENCODE project. Now I mistakenly downloaded huge 3.7GB file earlier and later on come to know that it is not the file I should use. Can someone please guide me. I know its a quite trivial thing but yet has kept me stuck.
What I Want
A file in which DNA/RNA data is placed as FASTA file. Sample is:
chr19:238,905 - 239,201 AGTCCGATGATGATAGATAGAGATTCCGATAGATGCGCGCGTGGGGTGATAGATG......
This is the link from where I want to download the file: https://www.encodeproject.org/experiments/ENCSR480LIS/
Thank you so much in advance. It may be a little thing for you but so important for me
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engineer.khan •
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If you want lncRNA sequences, then forget about Encode and just download lncRNA sequences (e.g., from RNAcentral).
Thanks! I tried lncRNAdb. But the thing confuses me is same lncRNA has different sequences for different experiment in their XML. For example I am pasting the XML of first entry in lncRNA in the XML file:
-<species>
<entry species="Homo sapiens (Human)">hg19 chr2:11534107-11543203</entry>
-<references>
<ref id="hg19 chr2:11534107-11543203">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr2:11534107-11543203</ref>
</references>
</species>
-<literature>
-<publication record="1">
<author>Ørom</author>
<pubmed>http://www.ncbi.nlm.nih.gov/pubmed/20887892</pubmed>
<title>Long noncoding RNAs with enhancer-like function in human cells.</title>
<year>2010</year>
</publication>
</literature>
-<sequence>
-<sequencerecord record="linc00570_homosapiens_1">
<species>Homo sapiens</species>
<fastasequence>CGGAAGAGTGGGACGTTATGGAACCTTCTCAGCTTATTCAGAGAGGCTTCTTCTTCCTATTTAGTCTCCCTCTGGCTTTCCCTGCTGGGATCTGGGTGGTAGAAGCAGCAGGGGGATCAACGAACAGGCTGAGCGCCAAGAAGCCTGAAGATTCCAGAATCTAGCGGGAAAAGCATTCAGAGTCAGAATGAGCCACTTCCAGCATCGATGGTGTCAGGTCAGGTCCTCTGGGTAGAAGAAATGGAGTCAGTTAGGAGTGCTGGAGACTGAGTAAGAGGTGGCAGCTGAGGCTTACTACCCCAGGAAAGGGATGCCACCAGAGAAGGCAGACAACCAAGATGGCGACTCTCAATTTTTGAGCTCCTAATTTTCTCATGTCAGACATAAGAAAAAAAAATATTTTTTAAAGAAAAAGCTTTAGGTTGCAAAAATCTAGGCCTTTCAACTTTAAAATCCTATTCTTGCAAGCCTTGGAGAATAAAGCTTATGCATAAACAGTAGATTTGGAAACAGAAATATGCCTAATTACCCAGAGCCATTCTTTCAATACGCCAGTGATTGTTTAAAGATTCTATAGGCTGGAGTCAATGGCAGGAGGCGGGTGGGAAAAGAGTCAAGAGGGAGGAGAGAAGAAGCAAGAGGGTTGGGTAGATATTGTCACATGACCCTGAGAGGAGGATTCTGGGTCAAACCCCTAGGGGGTTGTGTGTAATGGAGACTCCAGATCCATTTGGGAATCTGGCTCCAAAGAAGACTTCACCTTGCCTTCTGAGTGGAGCCCTGAAGTGGCAAGACTCATAGAATTCCCCCACGGGTCCACACAAGAGAGAATGAATAGAGAAGGCTGCGTGCTGGCTGGACCAAGGCAGCCTCGGGTGACACCACCACCACCACCGCCGCTGCCGCCATCGCCATCACCACTGCCGCTGCCATCACCGCCACCACCACCACCATCACCACCACCATCACCACATTATGGACAATAGCCCAATGTTTCCTGAGTTCCCTAGAGGGTTGAAAGAGAATAGGACCTAGAGAGATCACATAGTTGGGACAGGCACTCATTAATTTGATCCAATGACAAGAGACCAGATGGGAAGAAGGATGCCTTGAGAGATGTCAGTGTGCACCCATGGATAGAAGCAGCTGGTGACTGGGTACTTGGGAAGCCACATGGACACACACAAAGCTCCTGGAAGACGTTTTCAAGGAGTTGGGCTGTGCTGGGATCCAGAACTGGCTGAAGAAACCATGAGCTGACATAAAATTTCTGCCACCTAGCAGAATGGAGGCTCCATTTGGAAATTAAATTATATACTTAAAAAAACTA </fastasequence>
ENST00000417473</accession>
<accessionlinks id="ENST00000417473">http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000417473</accessionlinks>
</sequencerecord>
-<sequencerecord record="linc00570_homosapiens_2">
<species>Homo sapiens</species>
<fastasequence>AGAGCCCCAGAGGCAGAGCTGCCCAAGGCTTTGGGAGCCCACCTCTTGCATCACTGTGCCCTGGATGTGAGACGTGGAATCAAGGAGATTATTTTGGAGCTTTAAGACGTAATGGCACCCTGCTGGGTTTCAGACTTGAGTGGAGCCTGCAGCCTTTCTTTCGGCCGGTTTCTCCCTTTTGGAACGGGAGTATTTACCCAATGCCTGTACCCCCATGACGTGCCCGTGTCCCCTTCCTCCACCACAAGATTGTAAGTTTTCTGGAGCCTCCCCAGAAGCTGAGAAGAAGCTGCTATGCTTCCTGTTCAGCCTGCAGAACCGCCACTTCCAGCATCGATGGTGTCAGGTCAGGTCCTCTGGGTAGAAGAAATGGAGTCAGTTAGGAGTGCTGGAGACTGAGTAAGAGGTGGCAGCTGAGGCTTACTACCCCAGGAAAGGGATGCCACCAGAGAAGGCAGACAACCAAGATGGCGACTCTCAATTTTTGAGC </fastasequence>
ENST00000437795</accession>
<accessionlinks id="ENST00000437795">http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000437795</accessionlinks>
</sequencerecord>
Thank you so much!! I think I have found what I was looking for. Really really thanks