How to download hg38 for spliceAI

Hi everyone, this is my first post and I'm also fairly new to bioinformatics. I am trying to use spliceAI with the grch38 assembly and my question is:

1) The link provided on the github splice AI page to download the grch38 assembly downloads it as a gz file, and it seems to take forever to expand, and using gzip on it at the command line also says "gzip: standard input is a terminal -- ignoring".

Does anyone have a recommendation on how to expand it better / is there another file people know of that could be used here?

Thank you!!

assembly

• 1,378 views • link

written 5.8 years ago by ian_chiquier •

0 answers

No answers yet.

More posts like this

VG autoindexing error: Chromosome path not found in graph or haplotypes
written 2.2 years ago by l.dammer •

Hi everyone, I'm trying to map my data to the genome graph provided by the human pangenome project on github (https://github.com/human-pangenomics/hpp_pangenome_resources). While doing that I've …
ONT direct RNA sequencing
written 2.4 years ago by Karina •

I have ONT direct RNA sequencing data consisting of 958 fastq.gz files per sample. I need to merge all of these files into a single …
Why SpliceAI does not annotate variants in different transcripts as SpliceAI lookup does.
written 3.5 years ago by Manuel •

I can see how [SpliceAI lookup][1] provides splice annotation for the the main transcripts of the affected gene. For example for the variant > chr1 …
Trim_galore with gnu parallel
written 5.5 years ago by francesca3 •

Hi, I'm trying to paralize trim_galore. I followed what was written here [https://www.biostars.org/p/359116/][1], but I continue to get an error. Here, there is my code …
Command not found after pip install spliceai
written 5.8 years ago by ian_chiquier •

Hi everyone, I used pip install to install spliceai, but then when I try to use commands like spliceai at the command line it says …
GTF/GFF3 file compatible with (GRCh38/hg38)(hg38)
written 5.9 years ago by kanwarjag

I am using Reference genome -Human Dec2013 (GRCh38/hg38)(hg38) and gene model Homo_sapiens.GRCh38.101.gff3.gz however I get error saying chromosome naming is not matching. I know that …
Which genome fasta file and GTF file to be used in the RNA-Seq analysis
written 7.1 years ago by wangdp123

Hi there, There are two types of genome fasta files for human species from GENCODE database (https://www.gencodegenes.org/human/): 1. Genome sequence, primary assembly (GRCh38) - ALL: …
fastq.gz goes into gz cpgz loop
written 8.9 years ago by S0phia •

We used a sequencing service and they gave us a 100GB tar file to download. After downloading, I checked the md5sum code and it matches …
EIGENSOFT: CONVERTF ignoring samples
written 10.7 years ago by aritra90

Hi, the CONVERTF program in EIGENSOFT package is ignoring few samples and not calculating their principal components. I am seeing this in my terminal when …
News: Solid Software Tools: Denovo Assembly/Xsq Tools Pipeline Mirrored At Biostar
written 13.9 years ago by Istvan Albert

The **Solid Software Tools** website seems to have been abandoned by the vendor and the software that used to be hosted on the site is …