panyq357/hts-scripts

This directory contains some stand-alone scripts which might be useful.

• check_md5.py: find all md5 files in current directory recursively, check them and aggregate results.
• genbank_to_fasta_gff.py: convert a Genbank file to FASTA and GFF files.
• make_consensus.bash: make a new reference genome using ref FASTA and VCF.
• make_samples.py: find all FASTQ files in current directory recursively, make a samples.yaml suitable for reads2bwa.smk pipeline.
• minimap2_homo_fetch.bash: fetch sequence from ref FASTA, use minimap2 to find homologous sequence in target FASTA.
• gsea_io.R: some R functions to convert DESeq2 counts and coldata to GCT and CLS files that may suitable for GSEA (not tested).
• rename_bigwig_chrom.py: rename chromesome name in bigwig files.
• mid_to_vcf.py: convert .mid files (e.g. files in http://server.ncgr.ac.cn/RiceHap3/Genotype.php) to .vcf files.