User: Rashedul Islam

gravatar for Rashedul Islam
Reputation:
260
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Trusted
Location:
Canada
Website:
http://www.chibi.ubc.c...
Scholar ID:
Google Scholar Page
Last seen:
2 weeks ago
Joined:
6 years ago
Email:
r***********@gmail.com

Posts by Rashedul Islam

<prev • 42 results • page 1 of 5 • next >
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Comment: C: Enrichment Analysis in R
... You might need to rephrase this line " I would like to perform an enrichment analysis to check whether or not category A has a enrichment of cancer genes.". Do you want enrichment of category A over category B? You can also check this: [Statistical significance of the overlap between two groups of ...
written 19 days ago by Rashedul Islam260
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Comment: C: ChromHMM segmenting only 1 chromosome
... Can I see the 'hg38.chrom.sizes' file header? Try changing the `-p` to at least 1 instead of 0; see [here][1]. [1]: http://epigenomegateway.wustl.edu/support/2016washu/JasonErnst_WUSTL_ChromHMM.pdf ...
written 19 days ago by Rashedul Islam260
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Answer: C: fastq-dump error for restricted data from dbGAP
... I finally figured out the issue after email communications with sra team. I only had the download permission and therefore I was not able to extract raw sequences. I got the NGC file with full permission from my PI. The instruction was "The dbGaP repository key is only available from the dbGaP accou ...
written 19 days ago by Rashedul Islam260
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Answer: A: Can we compare peaks of different transcription factors when they were obtained
... If you are looking at which genes are targeted by TFs, you can confirm this by looking at the tracks for enrichment at the selected genes loci. IDR/p-value/FDR are very useful to identify the statistically significant peaks. There is no restriction which method to use, but try to be consistent. Sinc ...
written 21 days ago by Rashedul Islam260
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Answer: A: GSEA top genes vs all platform
... Instead of using pre-ranked with 50-100 genes, you can use entire set. Then check how many genes have core GSEA enrichment and are differentially expressed. ...
written 22 days ago by Rashedul Islam260
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Answer: A: How do I extract Fasta Sequences based on a list of IDs?
... You can use this: `while read line; do grep -A 5 "$line" fastaFile; done ...
written 22 days ago by Rashedul Islam260
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Answer: A: ChipSeeker Heatmap (y-axis)?
... They are spread because you plotter around the TSS. To see the difference you are expecting, plot the binding sites around the peak centers of peak1 instead of TSS. ...
written 24 days ago by Rashedul Islam260
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Comment: C: ChipSeeker Heatmap (y-axis)?
... I added the answer below. ...
written 24 days ago by Rashedul Islam260
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Answer: A: obtaining unique peaks in DiffBind
... As @igor mentioned, you can get 100% present in one group while being 0% present in the other using `bedtools intersect`. However, this binarization approach might not be a good solution since there are false positives and true negatives in peak calling. You can use multiple differential peak caller ...
written 24 days ago by Rashedul Islam260
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Answer: A: Drug to Target/Gene/Protein Interaction Databases
... A good review published earlier 2018 on this topic summarized the updates of databases and methods. Yongjun Zhu et. al; [Drug knowledge bases and their applications in biomedical informatics research.][1] Brief Bioinform. 2018 Jan 3. [1]: https://www.ncbi.nlm.nih.gov/pubmed/29304188 ...
written 24 days ago by Rashedul Islam260

Latest awards to Rashedul Islam

Scholar 19 days ago, created an answer that has been accepted. For C: fastq-dump error for restricted data from dbGAP
Good Answer 6 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 6 months ago, asked a question with at least 3 up-votes. For Drawing venn diagram in R
Popular Question 13 months ago, created a question with more than 1,000 views. For Matching gene id and extracting fasta sequences using shell script
Great Question 18 months ago, created a question with more than 5,000 views. For Cufflinks error: BAM record error: found spliced alignment without XS attribute
Teacher 18 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 23 months ago, created a question with more than 10,000 views. For Drawing venn diagram in R
Student 2.1 years ago, asked a question with at least 3 up-votes. For Drawing venn diagram in R
Great Question 2.5 years ago, created a question with more than 5,000 views. For Drawing venn diagram in R
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Popular Question 3.7 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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