Information required about analysis_set

[Huma Asif]

Hi there,

I have downloaded hg19 fasta from 

https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/

and hg19.bed from 

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

select assembly hg19

region genome

output format : bed

output filename : ucsc.hg19.bed

click get output

Unfortunately, there are many scaffolds not overlapping 

I am wondering if there is any bed file based on fasta file in 

hg19.p13.plusMT.full_analysis_set.fa.gz 

so my main quest is do you have bed file of     
hg19.p13.plusMT.full_analysis_set.fa.gz
this fasta

I am also facing problem with bed file of 

wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/hg38.analysisSet.2bit

I downloaded one from UCSC table browser but it doesnt seems to support

Please help me as I am in the middle of analysis and bed files are giving trouble

Huma

[Daniel Schmelter]

Hello Huma,

Thanks for contacting the UCSC Genome Browser support team.

I couldn't quite understand what you wanted from this BED file download. Table Browser is not intended for retrieving data about the assembly itself, moreso it allows people to investigate datasets and annotation tracks. The default is "knownGene" AKA "UCSC Genes", which may explain why your BED file output did not cover the entire assembly.

Did you want a file with the length of the contigs from the Fasta file, like this?

chr1 0 249250621
...

If so, a contig name and length file exists called chrom.sizes. You will have to filter out the "alt" and "fix" sequences if you want to match the analysis set. If you want a true BED file, you will also have to add a column full of start positions, "0", before the end position.

https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes

If this is not what you wanted, could you please provide more context for what kind of data you would like and what you intend to do with it.

I hope this was helpful. For further communication, please reply-all to gen...@soe.ucsc.edu. Those emails are archived in a public help forum. For private questions, you may send emails instead to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser

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