Closed le-ander closed 4 years ago
Hi,
what genome(s) are you using for the assembly ? I added a quick fix for a 1 genome assembly. You can try adding the genome as an argument in epi.ct.bld_mtx_fly
Like such: epi.ct.bld_mtx_fly('atac_v1_hgmm_500_fragments.tsv.gz', 'atac_v1_hgmm_500_fragments.tsv.gz.tbi', windows, genome='hg19')
And install episcanpy again using the GitHub version
This is the information I have on my sample:
"reference_annotation": "gencode.v28.basic",
"reference_annotation_gtf_url": "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.basic.annotation.gtf.gz",
"reference_assembly": "GRCh38",
"reference_assembly_accession": "GCA_000001405.15",
"reference_assembly_fasta_url": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz",
"reference_organism": "Homo_sapiens",
"reference_version": "1.1",
The top of my fragments.tsv looks like this:
chr1 10084 10326 GCACCTTAGCTTACCA-1 1
chr1 10091 10210 GCGCCAATCTTTCGAT-1 1
chr1 10101 10283 CGTTCCACATTTGGCA-1 1
chr1 10138 10197 ACAGGCCTCCAACCTC-1 1
chr1 10144 10190 TCAGTTTCATTGAACC-1 1
chr1 10150 10198 AAATGAGAGAACTCCT-1 1
chr1 10150 10203 GTAGACTAGCAACGGT-1 1
chr1 10157 10192 TAGCCCTGTGATAGAT-1 3
chr1 10157 10198 TCAGTTTCATTGAACC-1 1
chr1 10272 10543 GCAGCTGGTAAGGTCG-1 1
Looks like it's working now if I specify genome=None
. Nice!
I'm hitting another issue with build_mtx_fly() after overcoming the import issue. i have built windows using the following function: windows = epi.ct.make_windows(10000)
Building the feature matrix based on these windows unfortunately fails: