Open tAndreani opened 4 years ago
You should be fine to use a transcriptome reference downloaded from BioMart as detailed here: http://www.nxn.se/valent/2016/10/3/the-first-steps-in-rna-seq-expression-analysis-single-cell-and-other http://www.nxn.se/valent/2016/10/3/the-first-steps-in-rna-seq-expression-analysis-single-cell-and-other
Best,
Mike
On 13 Feb 2020, at 11:53, Tommaso Andreani notifications@github.com wrote:
Hello,
i am trying to download the fasta transcriptome from Gencode as suggested:
ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.transcripts.fa.gz
Unfortunately the link is compromised. My question is: can I use another annotation or this can create probolems? I know that gencode and UCSC or ensembl use different chromsomes annotation (chr1 vs 1 for example..). Or, if you have such annotation could you please provide a link from which I can download it?
Thank you in advance for any reply.
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Hi Mike,
thank you for your reply and for this awesome software. I would need Human as a model and this for example does not have Ensembl Transcript ID (as suggested by Valentine tutorial). Maybe in 4 years things changed. Please see the picture below:
Can I use maybe the Transcript stable ID?
Ah yes. "Transcript Stable ID" is equivalent.
Very best,
Mike
On 13 Feb 2020, at 13:11, Tommaso Andreani notifications@github.com wrote:
Hi Mike,
thank you for your reply and for this awesome software. I would need Human as a model and this for example does not have Ensembl Transcript ID (as suggested by Valentine tutorial). Maybe in 4 years things changed. Please see the picture below:
https://user-images.githubusercontent.com/6462162/74438429-71256f00-4e6a-11ea-8358-443ee49a7210.PNG Can I use maybe the Transcript stable ID?
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Hello,
i am trying to download the fasta transcriptome from Gencode as suggested:
ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.transcripts.fa.gz
Unfortunately the link is compromised. My question is: can I use another annotation or this can create probolems? I know that gencode and UCSC or ensembl use different chromsomes annotation (chr1 vs 1 for example..). Or, if you have such annotation could you please provide a link from which I can download it?
Thank you in advance for any reply.