LinXing Chen

Hi, thanks for reporting this issue. Did you have the same issue while running other samples?

Hi, thanks for your interest in COBRA. Could you please refer to Issue#22 regarding the usage of COBRA on whole metagenomes? Let me know if anything stated therein is unclear....

Technically, you could use COBRA before binning, this step will make some of your contigs/scaffolds longer, but the issue is you have to rerun the mapping for a new sequencing...

Hi, Thank you for your interest in COBRA. Unfortunately, I have no experience with Docker and have been pretty busy these days starting my own lab. I will try probably...

Hi, Thank you for using COBRA. Generally, if a COBRA "Extended_partial" sequence was recognized as "circularized" by CheckV because of DTR, then usually, the length of DTR is not equal...

Hi Alena, Thank you for your questions. 1. for input, both contigs and scaffolds are fine, the queries should be from the corresponding set, though. 2. there are two ways,...

Hi Alena, The results are NOT normal. Usually, you will see more Extended_partial counts. Could you please check your -f file? I wonder if their length has been filtered somehow....

That's so weird. Two things to check, (1) Did you use the same paried-end reads files for mapping as you did for assembly? (2) How big is the file "COBRA_end_joining_pairs.txt"?

The COBRA_end_joining_pairs.txt is big enough, indicating that many contigs share their ends. However, the number of Orphan end contigs is 71822, which makes no sense. Could you check if any...

I do not understand. For example, FH63-8-contigs_2032496, is this one of the contig headers in your -f fasta file?