User: wm

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wm130
Reputation:
130
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Location:
China
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1 day, 7 hours ago
Joined:
8 years ago
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w*******@gmail.com

Posts by wm

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Centrimo error: Template does not contain data section
... it works. Thanks! I tested, `ame` and `centrimo` commands failed in `meme 5.0.5` in `conda` version. ...
written 1 day ago by wm130
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Comment: C: get only reads that has multiple alignment on bowtie
... This is what I want, extracting multiple mapped reads from bowtie alignment. I have tested for SE reads. Also you can extract **unique** mapped reads. > From Xianjun Dong's post, alternative, we can use `NH:i:x` tag, or the `FLAG` tag for this purpose. > > `awk '{if (and($2,0x100)) print ...
written 11 days ago by wm130
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Comment: C: How to find out the insert size in RNA seq data
... changes in argument: `-in` here is an example output: ```bash $ bamtools stats -in aaaaaa.bam -insert ********************************************** Stats for BAM file(s): ********************************************** Total reads: 1367054 Mapped reads: 1367054 (100%) Forward str ...
written 5 months ago by wm130
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Comment: C: Content of T was larger than others in NSR-RNAseq data, why?
... It is an NSR-primed whole transcriptome cDNA library, you can find the details here: http://www.nature.com/nmeth/journal/v6/n9/fig_tab/nmeth.1360_F1.html ![enter image description here][1] [1]: http://p1.bqimg.com/578111/3ffb51d35e98f1a7s.png ...
written 3.0 years ago by wm130
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Content of T was larger than others in NSR-RNAseq data, why?
... I found a strange base content in an NSR-RNAseq data (SE60), T% was higher than all others (A.C.G), Can anyone tell, what's wrong with the data set? The fastqc output (default parameter) were shown below: Add: This data set was generated by Illumina HiSeq2000 Clip reads (TruSeq adapter Index), d ...
forum rna-seq written 3.0 years ago by wm130
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Answer: A: Pheatmap Annotation
... According to my understanding, you just want to change the name of annotation from `class1`, `class2` to `Exp1` and `Exp2`. The original figure like this: ``` 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: ...
written 4.3 years ago by wm130
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Answer: A: Difference Between Htseq-Count And Bedtools Multicov
... you can check your GFF/GTF file and htseq-count command line: 1. check the col-3 (feature field) of GFF/GTF file, that should contain "exon" 2. in your htseq-count command line: --type=FEATURETYPE, default is "exon" ...
written 4.4 years ago by wm130
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Comment: C: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
... Nice, this is what I want. by the way, it is fit for dUTP strand-specific RNA-seq. Here is another problem when I create Bedgraph files using these BAM files: (1) what if the length of reads (read1 + read2) shorter than the insert seq? what is your choice for the gap that not sequenced that will n ...
written 4.5 years ago by wm130
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Comment: C: Counting sense reads in bacterial paired-end RNA-seq data
... How can we tell the read counts on plus strand (-F 16)? what if we set the "--library-type fr-firststrand" or "--library-type fr-secondstrand"? what is the difference? ...
written 4.5 years ago by wm130
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Answer: A: Visualize Strand-Specific Rna-Seq : How To Differentiate Strands
... @Ann How can I show the strand-specific reads? This fig seems not a strand-specific alignment (both strand have almost the same reads). ...
written 4.5 years ago by wm130

Latest awards to wm

Popular Question 6 months ago, created a question with more than 1,000 views. For How Can Soap2Sam.Pl Be More Fast?
Great Question 2.0 years ago, created a question with more than 5,000 views. For Error When Install Samtools, Version `Zlib_1.2.3.3` Not Found
Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: Pheatmap Annotation
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: Pheatmap Annotation
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Pheatmap Annotation
Supporter 4.4 years ago, voted at least 25 times.
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Error When Install Samtools, Version `Zlib_1.2.3.3` Not Found

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