the latest human reference genome fasta file

Question

[hana]

Hi all

I would like to download the latest human reference genome (GRCH38) in fasta and gtf format for my RNA seq analysis. I would like to know which database is the beast,Genbank version 21 or ensemble?

Where can I get the fasta file of whole genome of ensemble version?

Is the below link below contains this file?

ftp://ftp.ensembl.org/pub/release-77/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz

Is there any difference between GenBank and Ensembl's alignment and annotation output result ?

Thanks in advance

[iraun]

You can download it from UCSC database: http://hgdownload.cse.ucsc.edu/downloads.html#human

[hana]

Hi all

I would like to download the latest human reference genome (GRCH38) in fasta and gtf format for my RNA seq analysis. I would like to know which database is the beast, Genbank version 21 or ensemble?

where can I get the fasta file of whole genome of Ensembl version?

Is the below link below contains this file?

ftp://ftp.ensembl.org/pub/release-77/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz

Is there any difference between Genbank and Ensembl's alignment and annotation output result?

Thanks in advance

Answer 1

[Manvendra Singh]

database is the beast?????

Yes, Its the one from ensembl.

You can download it from here, same way as you previously downloaded hg19 from UCSC

whole genome fasta

http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/

GTFs from

http://genome.ucsc.edu/cgi-bin/hgTables?

[hana]

Which file is contained the whole genome file? hg38.2bit?

Thank you

[Devon Ryan]

Just directly download the fasta file. There's no need to deal with 2bit.

[Manvendra Singh]

Exactly, hana was asking about .2bit so I wrote that he can convert them as well.

[zizigolu]

Sorry @Devon, from where I could find fasta file for each individual chromosome for hs37d5.fa ?

[GenoMax]

https://www.gencodegenes.org/human/release_5.html assuming you are referring to release 5. All releases can be found on this page at GENCODE.

[Manvendra Singh]

Yes, you need to convert it to fasta

You can get the utility program TwoBitToFa from here.

Once you downloaded it, you must change permissions first to allow it to be executed as a program.

Then you execute it from a terminal without arguments to see the options:

$ /path/to/twoBitToFa

twoBitToFa - Convert all or part of .2bit file to fasta
usage:
twoBitToFa input.2bit output.fa

[hana]

thank you very much

[hana]

Hi

I have already download the fasta and gtf files of hg38 from USCS database and run tophat.

But I have a problem with running cuffllinks . I got the below error

cufflinks  --GTF   genome.gtf   -o   /home/ra/cufflinks    /home/ra/accepted_hits.bam

[20:55:32] Loading reference annotation.
Error parsing strand (1) from GFF line:
uc001aaa.3    chr1    +    11873    14409    11873    11873    3    11873,12612,13220,    12227,12721,14409,        uc001aaa.3

Can you please tell me what dose it mean and how can I solve it

Thank you

[Devon Ryan]

That's not a GTF file. You have to explicitly set the output format to GTF, otherwise you'll get all of the table columns as is.