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6 days ago by
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11 days ago by
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14 days ago by
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Recent Replies
Comment: Difference between USCS exon coordinates and ensembl
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Yes, BED file, so this is zero-based and on Ensembl Viewer it is 1-based. So that is the reason.
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Following GenoMax comment
This is what you have
NODE_217_length_5488_cov_28.472321_g133_i0 # typical rnaSPAdes transcript header
Thi…
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Thank you so much for this. Yes, in this case I get all the SNPs.
I also have one more question:
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lncRNAs are usually fine to include in downstream analysis since they are generally not selected against in most RNA-seq library prep proto…
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Thank you very much!! I'm new to this subject and I believe your answer gave me a great idea of where to go next, thanks again!!
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You are likely best served by using `NCBI datasets` ([**LINK**][1]) or `EntrezDirect` ([**LINK**][2]) command line tools.
If you want to …
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You could try to create one: https://groups.google.com/g/trinityrnaseq-users/c/qPbWnLl4iY0
While this is from an unrelated software the so…
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Hi @atpoint,
I went to http://genome.ucsc.edu/cgi-bin/hgTables and did:
1. ![enter image description here][1]
then:
2. ![enter image…
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See also: https://www.biostars.org/p/9535550/#9536086
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Hi,
As an alternative, you could use [NCBI Datasets][1] for this task. NCBI Datasets allows users to retrieve metadata reports in JSON or…
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Thank you for the info! It turned out that running all 10k at once is actually faster than running one or two at a time!
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Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
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If you want to go that route, yes.
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What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
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