User: zhangdengwei

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zhangdengwei50
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1 week ago
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10 months ago
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z***********@genomics.cn

Posts by zhangdengwei

<prev • 42 results • page 2 of 5 • next >
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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 4 months ago by zhangdengwei50 • updated 4 months ago by Nicolas Rosewick8.6k
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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 8 months ago by zhangdengwei50
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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 8 months ago by zhangdengwei50
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low mapping rate with bowtie2 and BWA, but not blast
... Dear all, I'd like to align the WGS data derived from PE50 to the human genome with `BWA` or `Bowtie2`, but the overall mapping rate was as low as 40%. Below is my command. nohup bwa mem -t 48 GRCh38.bwa L01_5-8_1.fq.gz L01_5-8_2.fq.gz -o align.pe.sam & nohup time bowtie2 -k 1 -p 36 -x ...
alignment rna-seq sequencing written 8 months ago by zhangdengwei50 • updated 8 months ago by h.mon29k
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Comment: C: how to compute the insert size in SAM file
... my version of BWA is 0.7.17-r1188 ...
written 8 months ago by zhangdengwei50
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Comment: C: how to compute the insert size in SAM file
... My sequencing protocol is circle-Seq, which can be found in this [paper][1]. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924695/pdf/nihms866510.pdf ...
written 8 months ago by zhangdengwei50
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Comment: C: how to compute the insert size in SAM file
... I used BWA mem to align paired-end reads to reference genome. ...
written 8 months ago by zhangdengwei50
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how to compute the insert size in SAM file
... Dear all, I am confused about how the insert length (9th column) was computed in SAM file, for instance, the two PE50 reads below were aligned to reference genome, and the 4th column is 1-based leftmost mapping POSition for each read. For CL200085426L1C001R001_4504, the insert size should be equal ...
alignment written 8 months ago by zhangdengwei50 • updated 8 months ago by Biostar ♦♦ 20
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how to output the best alignment rather than multiple alignments for each read in BWA
... Dear all, I would like to use BWA mem to output the best alignment for each read instead of all alignments, just like the `"-k"` argument below in Bowtie2, however, I haven't found the same function in BWA mem, which my version is 0.7.17-r1188, did I miss something or how can I tackle it? -k ...
alignment written 8 months ago by zhangdengwei50 • updated 8 months ago by d-cameron2.1k
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Comment: C: how to fix the error - Too many open files - by changing code in python3.7
... Thanks! I found the below code can work, but I am still not clear about the cause, the dictionary shouldn't be sorted in the loop? match_dic = sorted(match_dic.items(), key=lambda item:item[1][-1], reverse=True) with open(offtarget_output, "w") as fo: with open(unmatch_output, ...
written 9 months ago by zhangdengwei50

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Popular Question 8 weeks ago, created a question with more than 1,000 views. For how to fix the error - Too many open files - by changing code in python3.7

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