Hello all,
Sorry if this has been posted before, but after searching the internet I seem to be at a dead end.
I currently...
16 results in 0.0022 seconds.
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Download all bacteria genomes in .gbk format
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Generate local blast database with RefSeq bacteria AND taxonomy
Dear all,
I would like to be able to create my own custom local blast database, as this may be relevant in many different situations in... -
GFF3 formatting wrong for RSEM?
Hello SEQanswers community,
When I run rsem-prepare-reference with refseq it only captures "tRNA" in my gff3 file. I only realized... -
refSeq gene tables -- all in one file?
Does NCBI have a single, downloadable file containing all refSeq-annotated exons for all genes? This information is available on a browser, one gene... -
Ensembl/NCBI/UCSC mouse gene annotations for cufflinks
Dear seqA community,
I'm assembling transcripts on the mouse reference annotations (*.gtf files) provided by Ensembl, NCBI and UCSC. Ideally,...Last edited by sp144; 11-30-2013, 05:46 PM. -
BED to RefSeq gene format
Hello,
I would like to convert a BED interval file to RefSeq format. I need this to use it among with GATK DepthOfCoverage.
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Get Promoter Sequence for List of RefSeq IDs
Dear All,
I have a list of RefSeq IDs. Each ID consists of a pair of IDs (protein ID;mRNA ID) for example (NP_001135412.1; NM_001141940.1).... -
Table of transcript variant 1
Hi all,
I really hope that someone could help me.
I would like to have a table that reports the information about the all the transcripts... -
Coding and non-coding transcripts overlap in databases, am I doing something wrong?
While working with the UCSC and RefSeq noncoding data extracted as instructed, I found a strange problem.
First of all, I collected non-coding... -
Drosophila Refseq
NCBI Refseq FTP doesn't have Drosophila sequences.
The problem with Flybase is that there is no single non-redundant database file for the entire... -
How do you download old RefSeq releases
If I need to run analysis using a specific release version of Refseq, is there a place to download it (say release 56)?
They are on release... -
Information about a gene
Hello everyone,
I want to get some information about a gene with a ensembleID (example: ENSG00000241635)
When I use the webbrowser,... -
lncRNA transcript databases for RNA-Seq analysis
Hello all,
I'm wondering if anyone has experience with or has seen a comparison of the various transcript databases (RefSeq, Ensembl, UCSC)... -
Non-species refseq genes in UCSC Genome Browser
Hi,
I am blat-ing sequences using the UCSC Genome Browser to see if the neighboring genes of certain sequences are conserved in different... -
Which annotation source is best?RNA-seq
Hi all,
From this presentation http://chagall.med.cornell.edu/NGSco...ass03_2010.pdf
I got this image
but...
