User: Rashedul Islam

gravatar for Rashedul Islam
Reputation:
350
Status:
Trusted
Location:
Canada
Website:
http://www.chibi.ubc.c...
Scholar ID:
Google Scholar Page
Last seen:
3 days, 18 hours ago
Joined:
7 years, 8 months ago
Email:
r***********@gmail.com

Posts by Rashedul Islam

<prev • 66 results • page 1 of 7 • next >
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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 5 days ago by Rashedul Islam350
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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 5 days ago by Rashedul Islam350
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Comment: C: bedtools bamtofastq: Segmentation fault (core dumped)
... > samtools fastq worked perfectly. ...
written 9 days ago by Rashedul Islam350
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bedtools bamtofastq: Segmentation fault (core dumped)
... I want to get all the reads from a bam file in a single fastq file. I am getting the message "Segmentation fault (core dumped)" while running bedtools bamtofastq -i in.name.sorted.bam -fq out.fq However, it works for the PE mode bedtools bamtofastq -i in.name.sorted.bam -fq out.R1.fq -fq ...
bedtools bamtofastq bam rna-seq written 9 days ago by Rashedul Islam350 • updated 9 days ago by h.mon29k
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from unmapped bam file picard samtofastq produced no output
... I generated bam of unmapped reads using: >$ samtools view -b -f 4 input.bam >unmapped.bam > >$ samtools flagstat unmapped.bam > > 2313037 + 4694809 in total (QC-passed reads + QC-failed reads) 0 + 0 > secondary 0 + 0 supplementary 0 + 0 duplicates 0 + 0 mapped > (0.00%:0.0 ...
bedtools picard rna-seq written 10 days ago by Rashedul Islam350
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Answer: A: what are the big questions in bioinformatics field nowadays
... To push the bioinformatics forward, please learn and improve the areas e.g., programming/algorithmic skills, understanding molecular biology and the ability to understand research papers. Bioinformatics is a big field and there are many problems to work on. If you can keep up with the current liter ...
written 5 weeks ago by Rashedul Islam350
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Comment: C: Alternative splicing event annotations method
... Thanks! I might give a try. ...
written 5 weeks ago by Rashedul Islam350
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Alternative splicing event annotations method
... Hi, I am looking for a computational method to identify the number of instances of each alternative event category listed below from RNA-seq data. I tried [MISO][1] but does not give the output I wanted. Any suggestion or link to any tool will be very helpful! The event categories: Skipped exo ...
miso rna-seq written 5 weeks ago by Rashedul Islam350 • updated 5 weeks ago by lieven.sterck7.2k
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Comment: C: Comparing values of a column if it falls between values of two columns of a diff
... If you can convert "B data set" as bed file, you could use bedtools intersect. ...
written 5 months ago by Rashedul Islam350
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Answer: A: Larger number of reads are aligned than input reads
... Same question [duplicated here][1]. [1]: https://www.biostars.org/p/326276/ ...
written 5 months ago by Rashedul Islam350

Latest awards to Rashedul Islam

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Matching gene id and extracting fasta sequences using shell script
Scholar 5 months ago, created an answer that has been accepted. For C: fastq-dump error for restricted data from dbGAP
Supporter 6 months ago, voted at least 25 times.
Great Question 11 months ago, created a question with more than 5,000 views. For Drawing venn diagram in R
Epic Question 20 months ago, created a question with more than 10,000 views. For Drawing venn diagram in R
Popular Question 20 months ago, created a question with more than 1,000 views. For Matching gene id and extracting fasta sequences using shell script
Popular Question 20 months ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Scholar 20 months ago, created an answer that has been accepted. For C: fastq-dump error for restricted data from dbGAP
Good Answer 2.2 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 2.2 years ago, asked a question with at least 3 up-votes. For Drawing venn diagram in R
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Matching gene id and extracting fasta sequences using shell script
Great Question 3.1 years ago, created a question with more than 5,000 views. For Cufflinks error: BAM record error: found spliced alignment without XS attribute
Teacher 3.1 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 3.5 years ago, created a question with more than 10,000 views. For Drawing venn diagram in R
Student 3.7 years ago, asked a question with at least 3 up-votes. For Drawing venn diagram in R
Great Question 4.1 years ago, created a question with more than 5,000 views. For Drawing venn diagram in R
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Popular Question 5.3 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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