Add uoHydFoet1 EAR #294
Add uoHydFoet1 EAR #294
Conversation
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Hi @tbrown91, thanks for sending the EAR of Hydrurus foetidus. |
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Hi @additive3, do you agree to supervise this assembly? |
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Hi @andar27, do you agree to review this assembly? |
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No |
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@andar27 Ok thank you, I will look for the next reviewer on the list :) |
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Hi @gitcruz, do you agree to review this assembly? |
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No |
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@gitcruz Ok thank you, I will look for the next reviewer on the list :) |
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Hi @tommathers, do you agree to review this assembly? |
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Thanks for agreeing! |
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This looks like a really difficult one. The coverage is also very choppy which makes it hard to interpret.
I had a look through and found the following:
SCAFFOLD_1: 1.277 Mb to 1.35 Mb Hap dup
SCAFFOLD_2: Scaffold_74 goes to gap at 11.6 Mb.
SCAFFOLD_3: 4.671 Mb to 4.842 Mb flips.
SCAFFOLD_4: Start to 368 Kb hap dup (it has some repeat but looks like prob alternative version from other hap, coverage is low). Also, 8.465 Mb to 8.5 Mb hap dup.
SCAFFOLD_5: Small hap dup between gaps at 6.5 Mb 6.53 Mb.Flip chunk from 6.27 Mb to 6.5 Mb.
SCAFFOLD_6: Flip chunk from 5.5 Mb to 6.15 Mb.
SCAFFOLD_8: Small hap dups between gaps at 5.78 Mb and 5.28 Mb.
SCAFFOLD_9: Small hap dup between gaps at 1.862 Mb and 1.893 Mb.
SCAFFOLD_9: SCAFFOLD_147 flips and places in gap at 4.5 Mb.
SCAFFOLD_10: not 100% but I would prob remove 5.7 Mb to 5.9 Mb as hap dup / false dup.
SCAFFOLD_14: Small hap dup at gaps at 1.65 Mb.
SCAFFOLD_15: 3.648 Mb to 3.673 Mb hap dup.
SCAFFOLD_16: start to 19 Kb hap dup. Also, 1.33 Mb to 1.37 Mb.
SCAFFOLD_18: Small hap dup at gaps at 3.8 Mb.
SCAFFOLD_19: flip from start to 1.862 Mb then move chunk from 0 to 44Kb to shrapnel, flip chunk from 1.868 Mb to 1.97 Mb. Small hap dup at 2.148 Mb.
SCAFFOLD_20: Scaffold_71 places in gap at 4.124 Mb
SCAFFOLD_22: Flip chunk from 3.234 Mb to 3.514 Mb. Small piece from 3.641 Mb to 3.692 Mb possibly change to unloc or put in shrapnel.
SCAFFOLD_23: Scaffold_92 places in gap at 82 Kb.
SCAFFOLD_24: 3.343 Mb to 3.362 Mb hap dup. Small piece right at end could prob go to shrapnel. Move chunk from 2,99 Mb to 3.063 Mb to end.
SCAFFOLD_27: small hap dup at 749 Kb.
SCAFFOLD_29: Flip chunk from start to 260 Kb.
SCAFFOLD_30: Hap dup at 718 Kb between gaps.ew
SCAFFOLD_33: cmall chunk from start to 33 Kb is hap dup.
SCAFFOLD_36: I think flipping from start to gap at 730 Kb looks slightly better. Also, although coverage is not 100 % conclusive I think unloc_1 is hap dup.
SCAFFOLD_39: I thin tiny bit from start to first gap is hap dup, then flip chunk from 12 Kb to 572 Kb.
SCAFFOLD_76, 77 etc. don’t have much background to main assembly but plssibly just because they are repetitive. I would blast them to double check not contamination.
Shrapnel hap dups: SCAFFOLD_151, SCAFFOLD_111, SCAFFOLD_203, SCAFFOLD_176 (there are prob some others).
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Thanks @tommathers Yeah, I didn't have much fun with this one. Thank you for your edits. I'll go through and hopefully get another map to you soon |
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Just some comments, and then I'll make a new HiC map for you. Thank you for going through so thoroughly, I really appreciate it.
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Re. SUPER_5. I think it looks better flipped once the hap dup where the marker is in this pic is removed. 
Then you can flip and get this: 
Good idea to check for mito in those high cov scaffolds. |
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Also, think there is a hap dup I missed on SCAFFOLD_6 @641 Kb. |
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Attention @additive3, the EAR PDF was updated. |
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Ping @additive3, |
2 similar comments
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Ping @additive3, |
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Ping @additive3, |
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Hi @tommathers not sure if you're back yet, but I made some changes to the map. Can you see if you're happy with the assembly? |
5 participants
Assembly review request