User: Rashedul Islam

gravatar for Rashedul Islam
Reputation:
370
Status:
Trusted
Location:
Canada
Website:
http://www.chibi.ubc.c...
Scholar ID:
Google Scholar Page
Last seen:
5 days, 12 hours ago
Joined:
8 years, 3 months ago
Email:
r***********@gmail.com

Posts by Rashedul Islam

<prev • 74 results • page 1 of 8 • next >
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Comment: C: Contigs have different mutations than raw reads
... The first one is megahit ($megahit -1 fastq1 -2 fastq2 -o /path/) and second one is metaspades ($metaspades.py -1 fastq1 -2 fastq2 -o /path/). Reads were trimmed with Trimmomatic. Its an RNA virus genome. ...
written 6 days ago by Rashedul Islam370
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Contigs have different mutations than raw reads
... Hi, I ran two assembly softwares and called mutations from the contigs. However, when I compared the contigs with raw reads, I found some instances where raw reads does not have mutations but the contigs have. I don't know how to explain this. Please see the attached. ...
assembly forum mutation calling written 7 days ago by Rashedul Islam370 • updated 7 days ago by Bastien Hervé4.8k
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Comment: C: Different assembler and difference in genomic variants. Is it possible?
... Yes, thats a great point. Thanks! ...
written 18 days ago by Rashedul Islam370
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Comment: C: Different assembler and difference in genomic variants. Is it possible?
... Its a ssRNA virus but not sure about clonality. Its almost impossible to have two different strains in the sample. ...
written 18 days ago by Rashedul Islam370
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Different assembler and difference in genomic variants. Is it possible?
... Hi, I assembled a viral genome using two different assemblers e.g., Megahit and Metaspades. Both the assemblers uses de bruijn graphs but might use different k-mers because both the assemblers uses multi k-mer approach. I aligned the contigs to the reference and called variants using BCFtools. I a ...
assembly written 18 days ago by Rashedul Islam370
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Answer: A: clusters generated by plotHeatmap of deeptools
... Please look at the Output Options [here][1]. You can use - > --outFileSortedRegions [1]: https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html#Output%20options ...
written 11 weeks ago by Rashedul Islam370
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Comment: C: Alternative splicing event annotations method
... I found this [review][1] that summarizes the tools used to find most of the alternative splicing events from RNA-seq. [1]: https://doi.org/10.1093/bib/bbz126 ...
written 5 months ago by Rashedul Islam370
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Comment: C: Log2 fold change correlation for ChIP seq data - do I need a FDR cut off?
... Why not applying thresholds for both fold-change and FDR? ...
written 5 months ago by Rashedul Islam370
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Answer: A: How to extract a fasta sequence from a batch of multiple fasta genome files
... If you know the gene id you can use [seqkit grep][1]. [1]: https://bioinf.shenwei.me/seqkit/usage/#grep ...
written 6 months ago by Rashedul Islam370
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Comment: C: How to round the "expected counts" to integers?
... If you mean to round floating numbers, you can use round() in R. ...
written 6 months ago by Rashedul Islam370

Latest awards to Rashedul Islam

Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Cufflinks error: BAM record error: found spliced alignment without XS attribute
Popular Question 8 months ago, created a question with more than 1,000 views. For Matching gene id and extracting fasta sequences using shell script
Scholar 12 months ago, created an answer that has been accepted. For C: fastq-dump error for restricted data from dbGAP
Supporter 13 months ago, voted at least 25 times.
Great Question 18 months ago, created a question with more than 5,000 views. For Drawing venn diagram in R
Epic Question 2.2 years ago, created a question with more than 10,000 views. For Drawing venn diagram in R
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Matching gene id and extracting fasta sequences using shell script
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Scholar 2.2 years ago, created an answer that has been accepted. For C: fastq-dump error for restricted data from dbGAP
Good Answer 2.7 years 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 2.7 years ago, asked a question with at least 3 up-votes. For Drawing venn diagram in R
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Matching gene id and extracting fasta sequences using shell script
Great Question 3.7 years ago, created a question with more than 5,000 views. For Cufflinks error: BAM record error: found spliced alignment without XS attribute
Teacher 3.7 years 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 4.1 years ago, created a question with more than 10,000 views. For Drawing venn diagram in R
Student 4.3 years ago, asked a question with at least 3 up-votes. For Drawing venn diagram in R
Great Question 4.7 years ago, created a question with more than 5,000 views. For Drawing venn diagram in R
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Popular Question 5.9 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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