User: caizexi123
caizexi123 • 40
- Reputation:
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- Location:
- Denmark
- Last seen:
- 1 year ago
- Joined:
- 3 years, 6 months ago
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Posts by caizexi123
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... Hi, you should directly write a email to them, tell them your scaffold N50 and so on. ...
written 17 months ago by
caizexi123 • 40
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... You can edit the assemble.sh script and decrease $JF_SIZE, in your case it will take much more than what you have. But to be honest, MaSuRCA will take more than 1.2TB. ...
written 20 months ago by
caizexi123 • 40
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Comment:
C: SSPACE file error
... You can try to change the aligner in the library file, for example, bowtie or bwasw.
I remember sometimes SSPACE will have some troblue with one of the aligners.
Or you can use older version of SSPACE. ...
written 20 months ago by
caizexi123 • 40
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... Hi,
First you should try to know how much percent of your genome is repeat and whether your sample is inbread line.
And there are some parameters will affect the result of assembly, you should try different parameters.
Also the pre-process,like trimed reads, remove contamination and error correct wi ...
written 20 months ago by
caizexi123 • 40
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... Dear all,
Hi!
Does anyone know which company of lab provide a good service for Optical mapping? ...
written 23 months ago by
caizexi123 • 40
• updated
23 months ago by
Daniel Swan ♦ 13k
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... No. The online service will do everything. The input is the full protein sequence of blind mole rate, the output is the orthologs groups for each protein. Then you can analyze which of the orthologs groups mouse have. ...
written 23 months ago by
caizexi123 • 40
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... If you have the all the blind mole rate protein sequences, you can use OrthogMCL online service, and you can extract all the orthologs with mouse ...
written 23 months ago by
caizexi123 • 40
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... A quick way to find out whether your data is mate-pair reads.
Circularized Duplicate Junction Adapter
CTGTCTCTTATACACATCTAGATGTGTATAAGAGACAG
Circularized Single Junction Adapter
CTGTCTCTTATACACATCT
Circularized Single Junction Adapter Reverse Complement
AGATGTGTATAAGAGACAG
using ' grep "one o ...
written 23 months ago by
caizexi123 • 40
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... The library construction for mate-pair and pair-end is different. And based on the insert size "500", it seems pair-end. So you either asked the people who sequenced the data or map your reads to close-relate species to estimate the insert size.
PS, you can run MaSurCA with pre-process data even the ...
written 23 months ago by
caizexi123 • 40
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... It seems the RAM problem, you even not yet generate the jellyfish output. You should check "error_correct.log". ...
written 23 months ago by
caizexi123 • 40
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For Error while abyss running on cluster
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