HiC得到的AGP文件翻译错误问题 2020-09-02
2020-09-02 本文已影响0人
SnorkelingFan凡潜
看示例：
- AGP文件其中一条
HiC_scaffold_1 646664 673414 11 W ctg6060_np512 1 26751 -
- 由AGP得到的gff对应的信息
HiC_scaffold_1 maker mRNA 665102 667305 . + . ID=augustus-ctg6060_np512-processed-gene-0.11-mRNA-1;
HiC_scaffold_1 maker CDS 666968 667305 . + 0 Parent=augustus-ctg6060_np512-processed-gene-0.11-mRNA-1;
HiC_scaffold_1 maker CDS 665102 666056 . + 1 Parent=augustus-ctg6060_np512-processed-gene-0.11-mRNA-1;
- 由2得到的HiC对应的gff进行翻译得到的pep
>augustus-ctg6060_np512-processed-gene-0.11-mRNA-1 [mRNA] locus=HiC_scaffold_1:665102:667305:+ [translate_table: standard]
EFTVEIPMCDLQUQPLTQRPHRAAEKUSHUNFKLHUVYCHUQMGYKUHSP
HDHHUFSDURPINIWVHYLGTSKUIUEKKAGNYLUUCTKICHWSSTVSYR
CTUKRSTTGKHGKUNQAPKUNVFDKKYGSHKHPFRKVHCKENWEQSERYF
KUFSSLPRGTUHQLQQHNUYSTGELPRRESLYNLHGRAUIPIQVFASRVH
SMTIQGTUARQMERALIDRLGRLQELQQNGDRGIUCUHGMRYRNNYSUNK
QYFHGRSLNSGTGYUUTCLSGIULSDQQRUPLCSHRSRLPRUKLPKVITR
LHHKLMTAAKKARSLTLCURCFGKRQCSRRNCHLYUKFYSPPPHPCSKFU
LPRGNSHUIRYSKSSPDRGCIDLPSTKCHLPGLUDRCTFRPMQQYYHCWU
SKFTPYLLGQTNRIRLVQVURCSFUGSNRCL
- 原始contig对应的pep
>augustus-ctg6060_np512-processed-gene-0.11-mRNA-1 [mRNA] locus=ctg6060_np512:18439:20642:- [translate_table: standard]
MVTLSHVPQGYSEALAVKIWIGECPLIIINIYVRKGYINTSWLNNIIKYS
KDPIIVMENFNIDISSNKNNPAHNVLEDWLLSINMRIMVGYVPIRIGYEG
SQSTIDFALMSSSNNSFHDNHFGFLPFRDSQAALIIIYEDLSTARKNKKF
IMACSMDISAAYDSVPIDKLMLKIIKMGIVGKVALWLNNFLNGREIRVKW
KNVYSKIAASNICVPQGSVLSPILFMIYMADLLEIFHRNVTILVYAEDIL
VYAIGNSNEEALNTLQNAIEEITKWCEAYDLMICPEKCTCINFTKSRKKA
LKEIRIEGVTIPWSSQLKFLCVIFNDNLSLKGHIEQLKNKVIKTLSYIKC
IATNKWGTNSTHLMTIINSVIRDQLTYGCTILAQANKSEKRKLETIYNNA
LRFAIGLPRYPIDVLRKEAQQASMEIESSS
看清楚了吗，hic得到的gff翻译和原始对应的完全不同，是什么导致的呢？
第1和第4原始的都是-方向，但是2、3都变成+的方向，进行翻译，自然错误了
