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BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
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Gencode Fasta link not available #46

Open tAndreani opened 4 years ago

tAndreani commented 4 years ago

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.

mstubb commented 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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tAndreani commented 4 years ago

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:

bracer

Can I use maybe the Transcript stable ID?

mstubb commented 4 years ago

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?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Teichlab/bracer/issues/46?email_source=notifications&email_token=AAIXBBUMENJEJRCVR6WSBCLRCVBGLA5CNFSM4KUQZ7MKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELU4URI#issuecomment-585747013, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIXBBQUI736CBBR5HEKQILRCVBGLANCNFSM4KUQZ7MA.