User: zhangdengwei

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zhangdengwei40
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8 months, 2 weeks ago
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z***********@genomics.cn

Posts by zhangdengwei

<prev • 39 results • page 1 of 4 • next >
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Unable to Visualize RGI results using JSON file upload
... 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 ...
rgi metagenomics card written 11 days ago by zhangdengwei40
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Comment: C: 'HTSeq._HTSeq.GenomicInterval' object has no attribute 'xrange'
... Yes, my version of `HTSeq` is 0.11.2, and 3.7 for `python` ...
written 6 weeks ago by zhangdengwei40
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'HTSeq._HTSeq.GenomicInterval' object has no attribute 'xrange'
... 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, "+") ...
htseq python rna-seq written 6 weeks ago by zhangdengwei40 • 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 zhangdengwei40
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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 zhangdengwei40
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DiffBind without replicates
... 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 ...
R diffbind chip-seq written 6 weeks ago by zhangdengwei40
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Comment: C: Calculate p-value for experiment group with replicates, while control group with
... 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 zhangdengwei40
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Calculate p-value for experiment group with replicates, while control group without replicates
... 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 ...
R deseq2 rna-seq edger written 12 weeks ago by zhangdengwei40 • updated 12 weeks ago by Nicolas Rosewick8.5k
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Comment: C: how to compute the insert size in SAM file
... 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 zhangdengwei40
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Comment: C: low mapping rate with bowtie2 and BWA, but not blast
... Thanks, I'm going to have a try, maybe there is something different. ...
written 6 months ago by zhangdengwei40

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