User: Rashedul Islam

gravatar for Rashedul Islam
Reputation:
220
Status:
Trusted
Location:
Canada
Website:
http://www.chibi.ubc.c...
Scholar ID:
Google Scholar Page
Last seen:
2 days, 23 hours ago
Joined:
5 years, 10 months ago
Email:
r***********@gmail.com

I am a Bioinformatics PhD student.

Posts by Rashedul Islam

<prev • 28 results • page 1 of 3 • next >
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Comment: C: which is good to study methylation among breast cancer patients; ChIP-Seq and Wh
... Two assays are very different and which one is best it depends on the question you are asking. If you have the option for only one, you can compare the cost, data size, computational requirement for downstream analysis etc. ...
written 10 days ago by Rashedul Islam220
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Comment: C: ChipSeeker Heatmap (y-axis)?
... What is the center of the heatmap? Can you rephrase your question? ...
written 10 days ago by Rashedul Islam220
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Answer: A: Ideas to split peaks into subpeaks - beyond PeakSplitter
... You can use [FindER][1] peak caller. This tool has the options for selecting minimum and maximum peak size. Along with it you can select the distance between two peaks to be merged together. [1]: http://www.epigenomes.ca/tools-and-software/finder ...
written 10 days ago by Rashedul Islam220
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Answer: A: Drug set enrichment analysis
... You can use GESA tool using preranked option. Details is [here][1]. [1]: http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/GSEAPreranked/1 ...
written 12 days ago by Rashedul Islam220
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Answer: A: Extract nucleotides from fasta file by a single position
... This should work. awk '{print $1 "\t" $2-1 "\t" $2}' input.file | bedtools getfasta -fi genome.fa -bed stdin -fo output.fa bedtools's getfasta is [here][1]. [1]: http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html ...
written 12 days ago by Rashedul Islam220
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Answer: A: Comparing Illumina with Affymetrix data
... Two relevant discussion on the question: 1. [Mapping Illumina Snp Ids To Rs Ids.][1] 2. [rs id comparison between genome version or build.][2] [1]: https://www.biostars.org/p/62337/ [2]: https://www.biostars.org/p/253350/#253352 ...
written 3 months ago by Rashedul Islam220
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Answer: A: RNA-seq heatmap output order
... #One example R code using pheatmap. library(pheatmap) #Input data data = matrix(rnorm(200), 10, 10) rownames(data) = LETTERS[1:10] colnames(data) = letters[1:10] #Stop clustering of rows to keep name orders according to the input. pheatmap(data, cluster_rows = F) ...
written 4 months ago by Rashedul Islam220
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Answer: A: How can I locate motif in DNA sequence.
... I found this tool (CIS-BP) that helps to do the job. Thanks all for your valuable suggestions. http://cisbp.ccbr.utoronto.ca/TFTools.php ...
written 6 months ago by Rashedul Islam220
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How can I locate motif in DNA sequence.
... I my ChIP-seq data, I used HOMER to call motifs. Now I have few regions of interest and I want to look at the DNA sequence which motifs are present. Any suggestion of tools how can I do this? I attached the following example from M. R. Mansour et al., Science (80). 346 (2014) to show what I want to ...
chip-seq written 6 months ago by Rashedul Islam220
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Answer: A: Match And Merge Information By Id In Two Files
... You can use dplyr in R as well. a = read.table("~/tmp/a.txt",header=T) b = read.table("~/tmp/b.txt",header=T) library(dplyr) inner_join(a, b) ...
written 12 months ago by Rashedul Islam220

Latest awards to Rashedul Islam

Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For C: Linux for loop for 2 inputs and 4 outputs for Trimmomatic fastq quality trimming
Student 3 months ago, asked a question with at least 3 up-votes. For Drawing venn diagram in R
Popular Question 10 months ago, created a question with more than 1,000 views. For Matching gene id and extracting fasta sequences using shell script
Great Question 15 months ago, created a question with more than 5,000 views. For Cufflinks error: BAM record error: found spliced alignment without XS attribute
Teacher 15 months ago, created an answer with at least 3 up-votes. For C: Linux for loop for 2 inputs and 4 outputs for Trimmomatic fastq quality trimming
Epic Question 20 months ago, created a question with more than 10,000 views. For Drawing venn diagram in R
Student 22 months ago, asked a question with at least 3 up-votes. For Drawing venn diagram in R
Great Question 2.2 years ago, created a question with more than 5,000 views. For Drawing venn diagram in R
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Cufflinks error: BAM record error: found spliced alignment without XS attribute

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