User: Rashedul Islam

gravatar for Rashedul Islam
Reputation:
310
Status:
Trusted
Location:
Canada
Website:
http://www.chibi.ubc.c...
Scholar ID:
Google Scholar Page
Last seen:
18 hours ago
Joined:
6 years, 12 months ago
Email:
r***********@gmail.com

Posts by Rashedul Islam

<prev • 50 results • page 1 of 5 • next >
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Comment: C: Reads and Read Segments in Alignment
... That worked for me. Thanks! ...
written 11 days ago by Rashedul Islam310
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Comment: C: BLAST database with local sequences
... That was very helpful, worked for me. ...
written 5 weeks ago by Rashedul Islam310
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Comment: C: counting number of CpGs that are methylated and unmethylated in a read of whole
... Thanks again. That was very helpful. ...
written 5 weeks ago by Rashedul Islam310
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Comment: C: counting number of CpGs that are methylated and unmethylated in a read of whole
... Thanks a lot for pointing me such a nice tool. The following command worked for me is: MethylDackel perRead hg38.fa wgbs.bam The output example is below. Can I interpret the output like that- read name, chr, start position of the read. For last two columns- there are 3 CpGs in those reads but ...
written 5 weeks ago by Rashedul Islam310
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counting number of CpGs that are methylated and unmethylated in a read of whole genome bisulfite data
... Hi all, I need to get the number of CpGs that are methylated or, unmethylated per read of WGBS data. I am trying the calculate PDR values as described [here][1]. So far I made some progress but need some help from you guys. I can see this methylated or, unmethylated Cs on IGV. But I was wondering ...
genome next-gen sequencing written 5 weeks ago by Rashedul Islam310
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Comment: C: How can I get the names of bams that were merged
... That was simple and worked. Command `samtools view -H my.bam | grep '@RG'`. Thanks! ...
written 11 weeks ago by Rashedul Islam310
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How can I get the names of bams that were merged
... I have a single bam file which was created by merging few other bam files. How can I get the names of bam files that were used during merging? Thanks! ...
alignment sequence written 11 weeks ago by Rashedul Islam310 • updated 11 weeks ago by Medhat8.4k
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Answer: A: BWA mem error: [bwt_restore_sa] SA-BWT inconsistency: seq_len is not the same.
... I had the same issue. Solved by creating the reference index using the same version of bwa that I used for alignment (bwa mem). Before I was using the reference index created by the older version of bwa and I was getting the above mentioned error while running bwa mem. ...
written 3 months ago by Rashedul Islam310
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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 11 months ago by Rashedul Islam310
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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 11 months ago by Rashedul Islam310

Latest awards to Rashedul Islam

Great Question 3 months ago, created a question with more than 5,000 views. For Drawing venn diagram in R
Epic Question 11 months ago, created a question with more than 10,000 views. For Drawing venn diagram in R
Popular Question 11 months ago, created a question with more than 1,000 views. For Matching gene id and extracting fasta sequences using shell script
Popular Question 11 months ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Scholar 11 months ago, created an answer that has been accepted. For C: fastq-dump error for restricted data from dbGAP
Good Answer 17 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 17 months ago, asked a question with at least 3 up-votes. For Drawing venn diagram in R
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Matching gene id and extracting fasta sequences using shell script
Great Question 2.4 years ago, created a question with more than 5,000 views. For Cufflinks error: BAM record error: found spliced alignment without XS attribute
Teacher 2.4 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 2.8 years ago, created a question with more than 10,000 views. For Drawing venn diagram in R
Student 3.0 years ago, asked a question with at least 3 up-votes. For Drawing venn diagram in R
Great Question 3.4 years ago, created a question with more than 5,000 views. For Drawing venn diagram in R
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Drawing venn diagram in R
Popular Question 3.9 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 Cufflinks error: BAM record error: found spliced alignment without XS attribute

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