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<p>Hi Charlie,</p>
<p>The cDNA file contains sequences from all transcripts resulting
from known, novel and pseudo gene predictions, whereas the ncRNA
file contains the transcript sequences corresponding to non-coding
RNA genes. While the sets of transcripts are produced by different
pipelines, providing the sets as separate files makes sense as
some users are more interested in only having noncoding sets over
coding, for example.<br>
</p>
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<p>Daniel<br>
</p>
<br>
<div class="moz-cite-prefix">On 05/05/2017 18:11, Charles Joseph
Murphy wrote:<br>
</div>
<blockquote
cite="mid:633F8A6C-A131-4310-B30C-F0C0E1ED7DE9@med.cornell.edu"
type="cite">
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charset=windows-1252">
To be more specific, why are these two files separate? Why not
just have one FASTA file? I’ am asking this question because I’ am
working with another individual on a python package for
downloading/managing Ensembl data (<a moz-do-not-send="true"
href="https://github.com/hammerlab/pyensembl" class="">https://github.com/hammerlab/pyensembl</a>)
<div class=""><br class="">
</div>
<div class=""><a moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/release-88/fasta/homo_sapiens/cdna//Homo_sapiens.GRCh38.cdna.all.fa.gz"
class="">ftp://ftp.ensembl.org/pub/release-88/fasta/homo_sapiens/cdna//Homo_sapiens.GRCh38.cdna.all.fa.gz</a></div>
<div class=""><br class="">
</div>
<div class=""><a moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/release-88/fasta/homo_sapiens/ncrna//Homo_sapiens.GRCh38.ncrna.fa.gz"
class="">ftp://ftp.ensembl.org/pub/release-88/fasta/homo_sapiens/ncrna//Homo_sapiens.GRCh38.ncrna.fa.gz</a></div>
<div class=""><br class="">
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On May 5, 2017, at 13:06, Charles Joseph
Murphy <<a moz-do-not-send="true"
href="mailto:chm2059@med.cornell.edu" class="">chm2059@med.cornell.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Hi,<br class="">
<br class="">
Just out of curiosity, why are the cDNA and ncRNA
sequences in separate FASTA files? Is this due to each
set of transcripts being produced via different
computational pipelines?<br class="">
<br class="">
Charlie<br class="">
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</div>
</blockquote>
</div>
<br class="">
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<br>
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<br>
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</blockquote>
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