User: cfarmeri

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cfarmeri150
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Japan
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Posts by cfarmeri

<prev • 55 results • page 1 of 6 • next >
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The Most Appropriate Statistical Test
... How to choose statistical test method appropriate to my experiment design? ------------------------------------------------------------------------ I have following RNAseq samples. (I know 2 replicates is not enough...) 1. WT : wild type (replicate1, replicate2) 2. mm : gene X mutant (replicate1, ...
rna-seq edger statistical test written 15 months ago by cfarmeri150 • updated 15 months ago by h.mon25k
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Any packages for normalization by read depth of the 75%tile gene?
... Hi, Biostars. I want to normalize read count data (by STAR) by read depth of the 75%tile gene like this [paper](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1974105). Anyone knows useful packages (R, python ,etc) ? (I tried by "scale" function in R, but couldn't do this.) thanks!! ...
next-gen rna-seq written 2.6 years ago by cfarmeri150
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Any materials explaining BWA and Bowtie algorithm?
... Hi, Biostars. I would like to understand main mapping tools's agorithm, especially BWA, Bowtie. Anyone know any materials (not source code, slide,etc) for my purpose ? Thanks. ...
genome sequencing rna-seq dna written 2.9 years ago by cfarmeri150 • updated 2.9 years ago by Nicolas Rosewick7.6k
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Comment: C: splice junction file for human(hg19)
... In tophat manual, when "you supply your own transcript annotation data", you should use "--raw-juncs." option. Normaly(i.e. when dont have our OWN transcript annotation data including splice junction interval), GFF or GTF annotation file includes splice junction informatin. ...
written 2.9 years ago by cfarmeri150
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Comment: C: Proper use of BWA-backtrack and BWA-MEM
... Thanks, Brian. I confused the 63-67bp is a value close to 70bp. First of all, I try BWA-backtrack algorithm. ...
written 2.9 years ago by cfarmeri150
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Proper use of BWA-backtrack and BWA-MEM
... Hi, Biostars. I have a set of Illumina GA2 paired-end fastq files. These reads of the fastqs has 76b length. Before mapping, I trimmed barcode sequence from 5' end of both 1st and 2nd reads, finally, the reads have 63-67bp length. BWA's author says following. ・reads < 70bp should be mapped ...
genome written 2.9 years ago by cfarmeri150 • updated 2.9 years ago by dariober10k
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Comment: C: How to analysis coordinate density in whole gnome
... thanks harold, your "this post" lint is not valid... ...
written 3.1 years ago by cfarmeri150
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Answer: A: How to obtain the length of coding regions for the list of genes?
... chr1 100000 101000 geneX . + if your bed file is like above, you can obtain gene length awk command awk 'BEGIN{OFS="\t"}{print $4,$3-$2}' ...
written 3.1 years ago by cfarmeri150
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Comment: C: How to analysis coordinate density in whole gnome
... I would like to analysis whether some of bed positions exist in specific region of genome. For example, The number of positions : 10000 Whole genome length : 1.0E+9 [bp] Assuming the above, 10 positions cluster in 1.0E+6 may be random distribution. On the other hand, 10 positions cluster in 1.0 ...
written 3.1 years ago by cfarmeri150
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Comment: C: How to analysis coordinate density in whole gnome
... You say bedtools cluster? http://bedtools.readthedocs.org/en/latest/content/tools/cluster.html ...
written 3.1 years ago by cfarmeri150

Latest awards to cfarmeri

Popular Question 15 months ago, created a question with more than 1,000 views. For How to describe this figure
Popular Question 16 months ago, created a question with more than 1,000 views. For How to describe this figure
Popular Question 18 months ago, created a question with more than 1,000 views. For How to describe this figure
Popular Question 18 months ago, created a question with more than 1,000 views. For These gene symbol are from where? What source?
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Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to describe this figure
Popular Question 2.7 years ago, created a question with more than 1,000 views. For how to remove adapter sequence in RNAseq fastq file from a paper.
Popular Question 2.8 years ago, created a question with more than 1,000 views. For how to remove adapter sequence in RNAseq fastq file from a paper.
Popular Question 3.0 years ago, created a question with more than 1,000 views. For how to remove adapter sequence in RNAseq fastq file from a paper.
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