User: Ct586
Ct586 • 530
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- 7 years, 5 months ago
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Computional biologist!
Posts by Ct586
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... Dear All,
I wonder if there is a way to annotate the function of transposons.
One way I got is using for the nearest genes of each transposon to represent the function of the transposon. I wonder if there are other methods? Or what should I pay attention to when using neareset genes representin ...
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... @ Sebastian Kurscheid: Sorry that `ADD REPLY` link is not working for me. I have added operating system information and double checked environmental variables. Currently I can not get `configure` finished successfully. The command for configure is `./configure --prefix=/home/ct/softwares/R-3.2.0_ins ...
written 3.4 years ago by
Ct586 • 530
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... Hi, all,
When I was configuring R (R-3.2.0 and R-3.1.1), I met the following problems.
```
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h pr ...
written 3.4 years ago by
Ct586 • 530
• updated
3.4 years ago by
Sebastian Kurscheid • 300
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... Anyway I think it is weird since it works fine for you. Maybe I will give bedtools 2.17.0 a try just for curiosity.
...
written 3.6 years ago by
Ct586 • 530
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... It is a great choice. Just before trying `bedops`, I found my coordinates are too large, which causing the problem. Anyway, I'd like to try `bedops` since I am attracted by its homepage.
...
written 3.6 years ago by
Ct586 • 530
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... Thanks! That's the problem. This may be a potential bug of `shuffleBed` since the bed file is generated using it with `-chrom` parameter given.
...
written 3.6 years ago by
Ct586 • 530
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... Thanks, the version I am using is bedtools 2.22.1.
...
written 3.6 years ago by
Ct586 • 530
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... I have met an weird error.
Here lists my two bed files
```
==> a.bed <==
chr1 645339590 645344590
chr1 645485603 645490603
chr1 646267584 646272584
chr1 651156159 651161159
chr1 652224601 652234601
chr1 654584466 654589466
chr1 656200028 656210028
chr1 658335720 658345720
chr1 672881471 6 ...
written 3.7 years ago by
Ct586 • 530
• updated
3.7 years ago by
Alex Reynolds ♦ 25k
0
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... That is a great way to pick unique alinments usually. But how to interpret the coexists of MAPQ 0 and XT:A:U in one alignment of bwa output? ...
written 6.5 years ago by
Ct586 • 530
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... I wonder if you tried this software package. The document is very short and lack of necessary information. I have not found a way to use it. Could you give some suggestions? ...
written 6.6 years ago by
Ct586 • 530
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