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Thanks, Daniel! Just curious.
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<div class="">On May 8, 2017, at 04:33, Daniel Murphy <<a href="mailto:dmurphy@ebi.ac.uk" class="">dmurphy@ebi.ac.uk</a>> wrote:</div>
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<p class="">Hi Charlie,</p>
<p class="">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 class="">
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<p class="">Daniel<br class="">
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<div class="moz-cite-prefix">On 05/05/2017 18:11, Charles Joseph Murphy wrote:<br class="">
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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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hammerlab_pyensembl&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=GICRZSoAhe2BP7YElyjRWX_F3-aMNOyyb_Yl8uN0BrA&s=GIJjM-enHhnVjsyPgqKnAlxEFHGW5P6rnAeu3BLL0Lc&e=" class="">https://github.com/hammerlab/pyensembl</a>)
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<div class=""><a moz-do-not-send="true" href="https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.ensembl.org_pub_release-2D88_fasta_homo-5Fsapiens_cdna__Homo-5Fsapiens.GRCh38.cdna.all.fa.gz&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=GICRZSoAhe2BP7YElyjRWX_F3-aMNOyyb_Yl8uN0BrA&s=TNfIosv92Hh6GwzohqA2ruN7G27AUTq-_1Kv5AF55cQ&e=" class="">ftp://ftp.ensembl.org/pub/release-88/fasta/homo_sapiens/cdna//Homo_sapiens.GRCh38.cdna.all.fa.gz</a></div>
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<div class=""><a moz-do-not-send="true" href="https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.ensembl.org_pub_release-2D88_fasta_homo-5Fsapiens_ncrna__Homo-5Fsapiens.GRCh38.ncrna.fa.gz&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=GICRZSoAhe2BP7YElyjRWX_F3-aMNOyyb_Yl8uN0BrA&s=liPZa_ztGt9sFJ1ud9-dqHkagtFW5MoBTkxBucozu4U&e=" class="">ftp://ftp.ensembl.org/pub/release-88/fasta/homo_sapiens/ncrna//Homo_sapiens.GRCh38.ncrna.fa.gz</a></div>
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<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>
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<div class="">Hi,<br class="">
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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="">
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Charlie<br class="">
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