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小木虫论坛-学术科研互动平台 » 生物医药区 » 分子生物 » 生物信息 » 提交全基因组序列
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shellyxss

金虫 (正式写手)

[求助] 提交全基因组序列 已有1人参与

各位大神  我在提交了全基因组序列以后 NCBI给我回复了这样一个文件 这是什么意思啊 应该怎么办呢

[] We ran your sequences through our Contamination Screen. The screen found
contigs that need to be trimmed and/or excluded. Please adjust the
sequences appropriately and then resubmit your sequences. After you remove the
contamination, trim any Ns at the ends of the sequence and remove any sequences
that are shorter than 200 nt and not part of a multi-component scaffold.

Note that hits in eukaryotic genomes to mitochondrial sequences can be ignored
when specific criteria are met. Those criteria are explained below.

Note that mismatches between the name of the adaptor/primer identified in the screen
and the sequencing technology used to generate the sequencing data should not be used
to discount the validity of the screen results as the adaptors/primers of many
different sequencing platforms share sequence similarity.


[] Some of the sequences hit primers or adaptors used in Illumina or
454 or other sequencing strategies or platforms.  Primers at the
end of a sequence should be removed. However, if primers are
present within sequences then you should strongly consider
splitting the sequences at the primers because the primer sequence
could have been the region of overlap, causing a misassembly.

Skipped 1 same as before; no new sequences to screen.
1 sequence with locations to mask/trim

Trim:
Sequence name, length, span(s), apparent source
Scaffold1_1        3953201        1405766..1405795        adaptor:NGB00733.1-not_cleaned

提交全基因组序列
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Always be curious about nature
1楼 2015-12-19 22:28:04
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黑藻先生

银虫 (小有名气)

【答案】应助回帖

引用回帖:
4楼: Originally posted by shellyxss at 2015-12-21 14:04:21
After you remove the
contamination, trim any Ns at the ends of the sequence and remove any sequences
that are shorter than 200 nt and not part of a multi-component scaffold.

这一段话我不太明白是 ...

是这样的，在你组装序列的时候有个scaffolding过程，这个过程会让一些应该存在碱基但碱基缺失的地方填上N（代表这个地方应该有东西但是暂时不知），这个Ns应该是这个意思

还有一个叫你把小片段（低于200nt的）和不属于scaffold的东西去掉


提前交需要处理一些东西的
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8楼2016-01-28 20:35:53
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likelich

木虫 (小有名气)
大体意思是去掉引物 载体和其他修饰序列 重新拼接后提交

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2楼2015-12-19 22:51:55
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shellyxss

金虫 (正式写手)
引用回帖:
2楼: Originally posted by likelich at 2015-12-19 22:51:55
大体意思是去掉引物 载体和其他修饰序列 重新拼接后提交

那是不是就是说1405766..1405795这部分应该去掉呀？
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Always be curious about nature
3楼2015-12-20 09:56:34
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shellyxss

金虫 (正式写手)
After you remove the
contamination, trim any Ns at the ends of the sequence and remove any sequences
that are shorter than 200 nt and not part of a multi-component scaffold.

这一段话我不太明白是什么意思
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Always be curious about nature
4楼2015-12-21 14:04:21
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