mira.tl.get_distance_to_TSS(): human genome equivalent for parameter : genome_file

[shaistamadad]

Hi, It is not clear to me what the mm10.genome.sorted file data represents in the following code from your tutorial. It appears to be the chromosome sizes? I want to run this analysis for a human multiome dataset- where can I find the equivalent information for human genome please?

mira.tl.get_distance_to_TSS(atac_main,
                            tss_data=tss_data,
                            peak_chrom='chr',
                            peak_start='start',
                            peak_end='end',
                            gene_id='geneSymbol',
                            gene_chrom='chrom',
                            gene_strand='strand',
                            gene_start='txStart',
                            gene_end='txEnd',
                            **genome_file='mm10.genome.sorted')

Would the following work for human genome?

chr1 248956422 chr2 242193529 chr3 198295559 chr4 190214555 chr5 181538259 chr6 170805979 chr7 159345973 chr8 145138636 chr9 138394717 chr10 133797422 chr11 135086622
chr12 133275309 chr13 114364328 chr14 107043718 chr15 101991189 chr16 90338345 chr17 83257441 chr18 80373285 chr19 80373285 chr20 64444167 chr21 46709983 chr22 50818468 X 56040895 Y 57227415

Thanks so much for your help.

[AllenWLynch]

Hi,

Here is where you can get chromsizes: https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/latest/hg38.chrom.sizes

In general, this is a good resource for genome metadata: https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/

AL

---

From: shaistamadad @.> Sent: Monday, February 7, 2022 6:23 PM To: cistrome/MIRA @.> Cc: Subscribed @.***> Subject: [cistrome/MIRA] mira.tl.get_distance_to_TSS(): human genome equivalent for parameter : genome_file (Issue #5)

Hi, It is not clear to me what the mm10.genome.sorted file data represents in the following code from your tutorial. It appears to be the chromosome sizes? I want to run this analysis for a human multiome dataset- where can I find the equivalent information for human genome please?

mira.tl.get_distance_to_TSS(atac_main, tss_data=tss_data, peak_chrom='chr', peak_start='start', peak_end='end', gene_id='geneSymbol', gene_chrom='chrom', gene_strand='strand', gene_start='txStart', gene_end='txEnd', **genome_file='mm10.genome.sorted')

thanks so much for your help.

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[shaistamadad]

thanks very much!