LaZy

@Huangxc01 the gmap2AlleleTable.pl can only extract gene name with key "Name" in the column 9 of reference.gff3, but as the file you post here, there no any "Name" in the...

The first thing need be checked is that the bam file for drawing heatmap was generated by mapping reads to contig level assembly, and the ID of contigs must match...

@Huangxc01 for the data you post here, it may caused by the line 72 in the ALLHiC_plot, that we remove the '_pilon' while adding contig to the dictionary when reading...

It seems that the "data" is an empty list, the first thing need be checked is that whether the chromosome list file empty or not, then remove npz file or...

@lilyynu please check the chromosomes are appeared in the allele_table, and the name of chromosome not start with "tig", "scaffold", "utg", "ctg". If so, rename it or modify the partition_gmap.py...

@lilyynu Sorry for my unclear answer, I mean the first column of allele table is the name of chromosomes and if they start with prefix among "tig", "scaffold", "utg", "ctg",...

@lilyynu maybe you can write the code below to extract.py and run it with command "python extract.py chrom.fasta prunned.bam out.bam", and check if the output bam is empty or not...

The command "samtools view -bt" means use the fai file generated with fasta file to create header and generate bam file, the error you have got may caused by the...

@rahulvrane would you please show me the full command and the orderings.list file which you used for ragoo2ALLHiC?

@ptranvan, did you use the latest version of ALLHiC_plot? And can you show your chrn.list and first lines of groups.agp here? Because from the informations you post, we found that...