• Difference between the Fasta files from UCSC and Gencode/Ensembl

    I would like to know if there is any difference between the genome build fasta files from UCSC an...

  • How to download gc5Base file for hg38?

    Hi,

    I would like to download GC percent data for hg38 for different window sizes, particularly 5...

  • Gene Expression for mRNA sequencing tutorial

    Hello,

    I am a physicist by training, and I am very comfortable programming and working in a UNIX...

  • UCSC Transcriptome File

    I'm looking for a UCSC Trascriptome file for hg19 and hg38 that can be used for psuedo and lightw...

  • GFFutils very slow at creating database file. Any Idea why..?

    Hi guys, 

    I've been exploring [gffutils](http://pythonhosted.org/gffutils/contents.html) lately....

  • GRCh37/38(NCBI) vs hg19/hg38(UCSC)

    Are there any major differences between the GRCh38 (NCBI) and hg38(UCSC) databases, aside from th...

  • I need to download a list of all human genes with their respective Ensembl gene name | transcription start site ..

    Hello,

    I'm new here and and I need help please !

    I need to download a list of all human genes  ...

  • Inconsitency between Ensembl Assembly converter and UCSC LiftOver

    I am using UCSC's liftover tool to port a number of genomic coordinates between hg19 and hg38. A ...

  • bwa mem - expected runtime?

    Hi everyone,

    I am running an alignment to the Anna's Hummingbird reeference genome using files o...

  • Alignment speed for small FASTQ files

    My access to a cluster is limited at the moment and I would like to know if the computations can ...

  • Displaying Different Sized Lines In Ucsc Genome Browser

    I'm new to using the UCSC genome browser, and I'm making a custom track of SNPs where I'd like th...

  • Should kallisto take hours to run?

    Hello,

    I'm trying to align some test .fastq files to a reference using kallisto.

    The reference ...

  • Error indexing genome with STAR

    Hi,

    I have fastq file with 68 mln. 100 nt SE reads from human sample. I want to align them to hu...

  • ENSEMBL annotation file for quantification: which file to use?

    Hello, question regarding gene quantification for RNAseq: I've used HISAT2 to align my reads agai...

  • Assembly Id to UCSC names

    Hi all:

    Another NCBI/UCSC question. I have all the assembly Ids such as:

    GCA_000001405.15

    GC...

  • Is There Such A Thing As A Ucsc Api?

    Firstly, is there any real difference between the data stored at UCSC and that at EnsEMBL? If so,...

  • How Do you find constitutive exons in Ensembl or UCSC

    How do you find exons annotated as constitutive from official source Ensembl or UCSC?

    I first tr...

  • hg38 annotation file (gtf) UCSC format

    Hey,

    Does anyone know how to get the annotation gtf file for hg38 assembly  UCSC format ?

    I loo...



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