Ucsc Fasta Download
Nevada Biernat
The /gbdb fileserver offers access to all files referenced by the Genome Browser tables, with serversin North America andEurope for faster downloads.Many files in the browser, such as bigBed files, are hosted in binary format. For example, in the hg38 database, thecrispr.bb and crisprDetails.tab files for the CRISPR trackcan be found using the following URLs:
- North American server:
- European server: -euro.soe.ucsc.edu/gbdb/hg38/crispr/
I would like to know if there is any difference between the genome build fasta files from UCSC and Gencode/Ensembl ? For example, is there any difference between the GRCh38/hg38 of UCSC to Gencode/Ensembl and similarly for mm10/GRCh38 of UCSC and Gencode/Ensembl ?
The genome is the same regardless the genome browser you use. The Genome Reference Consortium are the people behind maintaining the human (and other) assemblies. So GRCh38 = Genome Reference Consortium Human Build 38). However, there may be different status, versions of that sequence. In Ensembl, you have GCA_000001405.22 (this is th INSDC assembly ID) whereas in UCSC you have GCA_000001405.15. The latest version is GCA_000001405.23 and is available on the GRC site. Usually the different versions of GCA_000001405 have to do with the addition of patches (the ones to fix the sequence and the novel patches. What types of patches are there). Although the assembly is essentially the same (GCA_000001405) (but remember the patches), the mode of annotation is completely different between UCSC and Ensembl. This explains what you've seen for MECP2. UCSC has it as X:154,021,573-154,097,755 76,183 bp whereas Ensembl has it as X:154,021,573-154,137,103. The start of the gene did vary (note the gene is on the reverse strand). Transcript MECP2-015 (i.e. ENST00000631210.1) is the culprit for the extended 5' end. This transcript was manually annotated by HAVANA and incorporated by Ensembl during the merge between automatic and manual annotation pipelines, which gives rise to the GENCODE set of genes. So you can use the fasta file downloaded from NCBI/UCSC and the annotation file downloaded from GENCODE, but do make sure the version of the FASTA sequence is the same version the annotation was carried out. If you download the FASTA from Ensembl, you need not to worry, the version will be the same.
NOTES: There are 2 fasta records in the NEW build, therefore, I used the argument '2' to split the build into two files. Each file contains one FASTA record, chr0 and chr1. Also need to create .lft files (for step [3]) that describe the two sequences. If breaking the sequences into chunks using the 'size' parameter, just use the -lift option. Otherwise, need to make your own .lft files. For example, chr0.lft contains:
However, I have now come across a Fatal error: Exit code 1 () when I have tried to use the data_manager_sam_fasta _Index_builder tool using the DBKey I have created from the previous step (i.e mm10). The Dataset Information and standard error generated by the tool is below;
We will use STAR to index the genome fasta file we just downloaded. We highly recommend you read and refer to the STAR manual when doing your own RNA-seq work, as it explains the meaning of all of the many parameters that are essential to produce an accurate, reliable STAR alignment.
Unfortunately, as of right now, STAR needs us to ungzip the genome files. In order to save space, we recommend ungzipping both the fasta and the gtf files, and then re-gzipping the fasta once the genome generation step is done. We will need the unzipped gtf file later.
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