MetaCC eliminated many of my contigs

[xujialupaoli]

Hi, thank you very much for providing such a useful tool.
When I used it, I found that MetaCC eliminated many of my contigs during the analysis process.

`bwa index graph.fa

bwa mem -t 80 -5SP graph.fa 100strain_sin3C_hic_R1.fq 100strain_sin3C_hic_R2.fq > MAP.sam

samtools view --threads 60 -F 0x904 -bS MAP.sam > MAP_UNSORTED.bam

samtools sort --threads 60 -n MAP_UNSORTED.bam -o MAP_SORTED.bam

python  MetaCC.py norm -e DpnII --min-len 1 --min-mapq 0 --min-match 0 --min-signal 0 --thres 0 --cover    -v graph.fa MAP_SORTED.bam /home/work/normCC 

python MetaCC.py bin --cover -v graph.fa /home/work/normCC 
`

I have encountered an issue with my graph.fa file, which contains a total of 405,631 contig sequences. However, after performing the normalization process, the output contig_info.csv file only includes information for 190319 contigs, indicating that many sequences were filtered out during the process.

Additionally, I have 210,216 contig sequences that contain restriction enzyme sites. I would like to understand the reasons behind the filtering of these contigs. Could you please clarify the cause of this filtering and how I can retain these specific contigs in the output?

Thank you for your assistance.

[dyxstat]

Hi,

Thanks for your interest in our MetaCC pipeline.

There is intricate filtering, which will filter contigs with within-contig Hi-C contacts equal to zero.

See row 384 in the script raw_contact.py:

if _sig[i] >= self.min_signal and _diag[i]>0 and self.seq_info[i].sites>0:

Best