User: zhangdengwei
zhangdengwei • 40
- Reputation:
- 40
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- New User
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- 1 week, 1 day ago
- Joined:
- 8 months, 2 weeks ago
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- z***********@genomics.cn
Posts by zhangdengwei
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... Hi,
I took advantage of online `CARD` to visualize the JSON file generated by command-line `RGI` with metagenomic sequencing data, but I failed. Here is my code:
nohup rgi bwt --read_one ../../05.kneaddata/${i}/Clean_*_kneaddata_paired_1.fastq --read_two ../../05.kneaddata/${i}/Clean_*_kneadda ...
written 11 days ago by
zhangdengwei • 40
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... Yes, my version of `HTSeq` is 0.11.2, and 3.7 for `python` ...
written 6 weeks ago by
zhangdengwei • 40
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... Hi,
I'd like to employ HTSeq to summarize my alignment data. But I encountered an error about its syntax, my code is
import HTSeq
ga = HTSeq.GenomicArray("auto", stranded=False)
iv = HTSeq.GenomicPosition('chr1', 50, "+")
ga[iv] += 1
iv = HTSeq.GenomicPosition('chr1', 50, "+") ...
written 6 weeks ago by
zhangdengwei • 40
• updated
5 days ago by
Biostar ♦♦ 20
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Comment:
C: DiffBind without replicates
... So sorry! I would keep it in mind. Thanks for your reminder. ...
written 6 weeks ago by
zhangdengwei • 40
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Answer:
A: DiffBind without replicates
... I got the answer from the developer of `DiffBind`. as follows
*Yes, replicates are required to do any kind of statistical analysis. Replicates are required to estimate the variance in the data and calculate confidence statistics such as p-values/FDRs.
Without replicates, you can do some explorator ...
written 6 weeks ago by
zhangdengwei • 40
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... Hi,
I am finding the differential peaks using `DiffBind`, but my sample has no replicates. And my `SampleSheet` is
> dbObj <- dba(sampleSheet="SampleSheet.csv")
trisomy_21 fibroblasts trisomy_21 trisomy_21 trisomy_21 1 narrow
euploid fibroblasts euploid euploid euploid 1 narrow
...
written 6 weeks ago by
zhangdengwei • 40
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... Thanks for your detailed explanation and I learn a lot. In my study, A is the patient with trisomy 21 and B is normal. I am confused about why the dispersion in A is probably much larger than in B if A is a cancer sample, may you explain it more? Thanks very much. ...
written 12 weeks ago by
zhangdengwei • 40
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... Hi,
I am a novice for bioinformatics. I have a simple question on how to calculate the pvalue for my RNA-Seq data, which has condition group with replicates and control group without replicates, like the following,
Condition: A1, A2, A3
Control: B
Sample with replicate is must for **DESeq ...
written 12 weeks ago by
zhangdengwei • 40
• updated
12 weeks ago by
Nicolas Rosewick ♦ 8.5k
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... Yes, thanks. I have used that software to deal with my data, due to a slight difference between circle-seq data and mine, so I had altered the analysis method in order to fit my own data. ...
written 6 months ago by
zhangdengwei • 40
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... Thanks, I'm going to have a try, maybe there is something different. ...
written 6 months ago by
zhangdengwei • 40
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