User: xieshaojun0621

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Posts by xieshaojun0621

<prev • 31 results • page 1 of 4 • next >
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Comment: A: Why chromosome coordinates were given for unmapped reads in hisat2?
... I think you are right. Here are the alignment information for both reads: ``` HWI-ST845:121014:C17LHACXX:8:1101:10013:60438 137 19 37413559 60 50M = 37413559 0 GTTGACAACAGTCTTGTCCAAGGGGATATCCACAGAGTACCTTGTGGGCA CB@FFFFFHHHHHJJJJJJJJJJJJGIIJIJJJJJJJFGHIJJJHIIJJD AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 ...
written 3 months ago by xieshaojun062190
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Why chromosome coordinates were given for unmapped reads in hisat2?
... Same question was also posted here: https://github.com/infphilo/hisat2/issues/125 Briefly, when I was trying to extract unmapped reads from hisat2 results using `samtools -f 4`. I got the alignment result like below: ``` HWI-ST845:121014:C17LHACXX:8:1101:10013:60438 69 19 37413559 ...
unmapped alignment rna-seq hisat2 written 3 months ago by xieshaojun062190
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Add labels in the annotation bar of pheatmap
... I have the code below to generate the heatmap with annotation. ![enter image description here][1] library(pheatmap) # Generate some data test = matrix(rnorm(200), 20, 10) test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3 test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10 ...
labels annotation pheatmap heatmap written 5 months ago by xieshaojun062190 • updated 3 months ago by SplitInf0
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Differences of taxid and species_taxid in assembly_summary.txt
... In the file I downloaded here (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt ), there are two columns: taxid and species_taxid **What's the difference between these two columns?** Some of the lines these two columns are different: 391008 40324 Stenotrophomonas maltoph ...
genome assembly refseq ncbi written 6 months ago by xieshaojun062190
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Answer: A: KOBAS web server
... Once I also encountered the same problem. They fixed the problem after I sent an email to the author. At that time, they responded me very quickly. Currently Chinese New Year is there. Maybe they won't respond your email in the next couples days. ...
written 11 months ago by xieshaojun062190
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Answer: A: Integrating DMR data
... If you know how to use Linux, you can install BEDTools and use intersectBed to accomplish your task. ...
written 22 months ago by xieshaojun062190
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How to extract all the terms using summary?
... Hi there! I'm using clusterProfiler to do KEGG enrichment analysis. The function "enricher" was used. `res <- enricher(geneList, TERM2GENE=term2gene, TERM2NAME=term2name, pvalueCutoff = 1, pAdjustMethod = "BH", qvalueCutoff = 1)` Then the function "summary" was used to extract the results. `s ...
clusterprofiler written 22 months ago by xieshaojun062190 • updated 22 months ago by Guangchuang Yu2.0k
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Comment: C: How to define a non differentially expressed gene?
... Thanks for your response. But do you have any suggestions of how to achieve my goal? ...
written 22 months ago by xieshaojun062190
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Comment: C: Scaling data using Pheatmap
... Here is the functions in the [code][1] : scale_rows = function(x){ m = apply(x, 1, mean, na.rm = T) s = apply(x, 1, sd, na.rm = T) return((x - m) / s) } As you can see, scale in this package means removing the mean (centering) and dividing by the standard deviation ...
written 22 months ago by xieshaojun062190
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Comment: C: Scaling data using Pheatmap
... Why do you think pheatmap scales the data to mean 0 and standard deviation 3? ...
written 22 months ago by xieshaojun062190

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