Hi,
I would like to ask for some opinion and advice related to the different available GTF-file sources for annotated genes.(mm10, but...
30 results in 0.0023 seconds.
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Problem with UCSC GTF files?
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Problem with UCSC GTF files??
Hi,
I would like to ask for some opinion and advice related to the different available GTF-file sources for annotated genes.(mm10, but... -
UCSC Encode files issue with MAPQ and Flags
Hi,
I have been reading Seqanswers for quite some time, but this my first question.
Does someone has experience with BAM... -
Extraction of BigWig data from UCSC
Hi,
I have a set of big wig files for ChIP-seq data and im looking to extract the values over a set genomic interval. However I have over 170 different... -
Differential expression gene list from TCGA level 3 RNASeq V2 datasets downloaded fro
I am interested in calculating differential expression of genes for tumor vs. normal samples from RNASeq V2 level 3 datasets for TCGA (downloaded from... -
Chromosome sizes don't match
Hi,
I'm having a heck of a time finding the chromosome sizes for mm9 that match the mm9 Bowtie pre-built indexes on their website. I... -
UCSC kgID string format
Hello all, this is my first post in SEQanswers.
You see, kgIDs appear like uc011mwm.1, uc011mwn.1, uc001adr.2, uc001ahe.3, etc. I'm wondering... -
displaying 454 data on ucsc
How can i display the 454.bam file on the ucsc custom tracks?
I have the contigs.bam file from the 454mapper software. Thare is no index file... -
Fetching minimal \ maximal transcription position per gene for UCSC\RefSeq
Hi,
I'm working with two gene tables (the UCSC knowngene table and the RefSeq refGene table) - the user of my program will choose which... -
GenomicFeatures: makeTranscriptDbFromUCSC suddenly started creating errors
I've been using the makeTranscriptDbFromUCSC function to retrieve ensembl genes from UCSC for over two years as part of our RNA-Seq expression profiling... -
Obtaining genomic features from miRNA-seq data based on UCSC hg19 alignment results
I have miRNA-seq data (single end) which I map to the whole UCSC hg19 genome. Now given the SAM output of this mapping, what's the good pipeline to summarize...Last edited by foolishbrat; 01-29-2014, 05:30 AM. -
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. -
get Gene Coordinates of human genes names
Dear all,
I have list of gene names, for example, the first five of them are:
ABCB1
ABCG2
ACHE
ACVR2A
... -
downloading human conservation scores for genomeGraphs
I have been using genomeGraphs in R and would like to analyze/visualize conservation scores for certain human genomic regions. In the vignette, phastCons... -
RepeatMasker track UCSC in R
Hi,
I have problems loading the repeatmasker track from UCSC into R. I try to use the makeFeatureDbFromUCSC function from the GenomicFeatures...
