59a3fbdf64e44ac8eac50f55e269004e5c09d397 markd Thu Jun 29 18:27:54 2023 -0700 added information on how CHM13 cytobands are built diff --git src/hg/makeDb/doc/hs1/t2t-supplied.txt src/hg/makeDb/doc/hs1/t2t-supplied.txt index 413394e..4d01661 100644 --- src/hg/makeDb/doc/hs1/t2t-supplied.txt +++ src/hg/makeDb/doc/hs1/t2t-supplied.txt @@ -53,36 +53,41 @@ Supplied by Savannah Hoyt <savannah.klein@uconn.edu> /team-epigenetics/PROseq-RNAseq_chm13v1.1/MappedToCHM13v1.1/RNAseq_Bowtie2/ renaming files to something not as long CHM13_S182-183_rnaseq_cutadapt-q20-m100_bt2-chm13v1.1_F1548.bigwig -> RNAseq_default.bw CHM13_S182-183_rnaseq_cutadapt-q20-m100_bt2-k100-chm13v1.1_F1548.bigwig -> RNAseq_k100.bw CHM13_S182-S183_rnaseq_cutadapt-q20-m100_bt2-k100-chm13v1.1-F1548_meryl-21mer-chm13v1.1.bigwig -> RNAseq_k100_21mer.bw RNAseq_k100_AB.markersandlength_meryl-21mer-chm13v1.1.bigwig -> RNAseq_k100_dual_21mer.bw lngbdb rnaseq/*.bw ================================================================ cytoBandsMapped (2022-02-22 markd) ---------------------------------------------------------------- cytoBand tracks from T2T project mapped from GRCh38 -Supplied by Nick Altemose <nickaltemose@gmail.com> -Delivered via Slack -trackData/cytoBandMapped +Supplied by Nick Altemose <nickaltemose@gmail.com>, <altemose@stanford.edu> +Delivered via Slack, but available from +https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v2.0_cytobands_allchrs.bed + +This track was generated using liftOver using the T2T GRCh38/hg38 minimap2 +liftover alignments and manually modifying them, as described in +chm13v2.0_CytoBandMapping.xlsx bedToBigBed -type=bed4+1 -as=${HOME}/kent/src/hg/lib/cytoBand.as chm13v2.0_cytobands_allchrs.bed../chromAlias/ucsc.sizes.txt cytoBandMapped.bb +trackData/cytoBandMapped lngbdb cytoBandMapped/*.bb ================================================================ sedefSegDups (2022-02-24 markd) ---------------------------------------------------------------- Supplied by Mitchell Robert Vollger <mvollger@uw.edu> team-segdups/Assembly_analysis/SEDEF/T2T-CHM13v2.SDs.bed bedToBigBed -as=${kentDir}/src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/schema/sedefSegDups.as -type=bed9+ T2T-CHM13v2.SDs.bed../chromAlias/ucsc.sizes.txt sedefSegDups.bb lngbdb sedefSegDups/*.bb ================================================================ rdnaModel (2022-03-02 markd) ----------------------------------------------------------------