Comments (7)
@smallfishcui Yes, it seems to be too few kmer markers. Do you have try the parameters -q 100
or -q 50
? Reducing -k
is not always a good idea and -disable_ltr
will result in no LTR, isn't it? I prefer that you can provide all the figures.
An explanation is that your species is not an extreme allopolyploid or the polyploidy event is too old.
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[Uploading k13_q100_f2.0.kmer_pca.pd
k13_q100_f2.0.kmer.mat.pdf
f…]()
I did the LTR searching but no LTR was found the the run just finish incomplete...so I skipped it to get the circos plot. It looks like my species is an allopolyploid of two closely related species, with only a few chromosomes differed. That is probably the reason why there are so few differed Kmer. Here are more plots: I will try longer kmer...the wgs suggests best kmer maybe around 30. i will keep you updated
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OK. Do you mean "there is no LTR" or "there is no subgenome-specific LTR"? The later is possible as there are so few subgenome-specific kmers, in which case you can just -disable_ltrtree
. I agree with you that it may be an allopolyploid of two closely related species or populations. It looks like the case of Cleistogenes songorica that can be found in our paper. You can try to reduce -q
to 20 - 50 to retrieve more differential kmers (but maybe more noisy).
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Thank you Rengang for the prompt reply! Yes, exactly as you said, there is no subgenome specific LTR detected. I will take a further look at the case of Cleistogenes songorica, and try different kmers. I will let you know how it goes shortly
best,
Cui
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Hi Rengang,
I've been trying using several Kmer size and q to analyze the subgenomes, and it seems indeed a similar case with Cleistogenes songorica. Neither longer kmer or lower counts improves the phasing. I guess it is possible that part of the subgenomes collapsed during the assembling process. please see some pics below, they are K13_Q20, K13_Q50,K13_Q100,K30_Q50,K31_Q5,K31_Q100:
![k13_q100_f2 0 circos](https://user-images.githubuserc
ontent.com/41078885/198015938-cbd1bb55-533f-4004-81d5-d5903d89023d.png)
![k31_q5_f2 0 circos](https://user-images.github
usercontent.com/41078885/198016021-5f6eac26-ad7f-4e38-9b63-278046e5f11f.png)
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@smallfishcui If there are indeed many assembly errors, such as switch errors between subgenomes, they should be first corrected.
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Yes, that's my aim to use subphaser. At first I don't know which chromosomes belong to one subgenome, and I kind of sorted it out after using subphaser for multiple times - although the results are not perfect it is also expected. However, this is not a problem of your program, and it really helped a lot already. I will proceed with downstream analysis and get back to you if there is further questions. Thanks!
best,
Cui
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Related Issues (20)
- Error in os.link(figfile, dstfig) HOT 3
- IndexError: cannot do a non-empty take from an empty axes. HOT 10
- Failed to install SubPhaser HOT 9
- ModuleNotFoundError: No module named 'TEsorter' HOT 4
- The output subgenomes are not paired HOT 4
- Changing mutation rate HOT 1
- Invalid specifier: '>=3.6:' HOT 1
- Only one pair of homologous chromosomes were not phased HOT 5
- matplotlib raise RuntimeError ('Invalid DISPLAY variable') HOT 2
- Unbalanced of chromosomes number and differential kmers number among subgenomes HOT 1
- `TEsorter` cannot find `rexdb` in Singularity container HOT 3
- Singularity container fails if environmental variable `R_LIBS_USER` is set HOT 2
- No differential kmers HOT 2
- ValueError: All singletons are not allowed HOT 1
- ValueError: 0 kmer with fold > 2. Please reset the filter options. HOT 1
- cannot allocate memory HOT 13
- 亚基因组分析 HOT 2
- Getting location of subgenome specific TEs HOT 2
- Suggestion for specific settings to improve subphasing HOT 3
- kmer 13 or less gives a lot of broken pipe errors HOT 5
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