User: irfanwustl

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irfanwustl0
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Posts by irfanwustl

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Bedtools intersect with header file
... Got it. Yes, the header was not indicated by '#' ...
written 7 weeks ago by irfanwustl0
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Comment: C: All CpG position of hg38
... Thanks. I have responded there. However, I was looking for all CpG sites. Not only the island. Is there any annotation for all CpG? ...
written 7 weeks ago by irfanwustl0
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Comment: A: Bedtools intersect with header file
... Sorry for my late response. Actually, I could not resolve it. Is it a bug? ...
written 7 weeks ago by irfanwustl0
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All CpG position of hg38
... I am looking for all CpG sites. Is there any bedfile which contains all CpG positions for hg38? ...
sequence cpg written 7 weeks ago by irfanwustl0 • updated 7 weeks ago by Kevin Blighe63k
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Bedtools intersect with header file
... I have two bedgraph files(a_h.bedgraph and b_h.bedgraph) with header. And I am running the following command: > bedtools intersect -header -wa -a a_h.bedgraph -b b_h.bedgraph However I am getting the following error: > Error: unable to open file or unable to determine types for file a_h.be ...
bedtools written 8 months ago by irfanwustl0 • updated 7 weeks ago by Alex Reynolds30k
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Answer: A: cram to bam conversion
... Solved. Seems it is a threading issue. When I have removed > -@8 from the code, there is no error or warning. ...
written 10 months ago by irfanwustl0
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Biscuit: Is alignment stochastic?
... I have WGBS pair-end fastq files. I am using [Biscuit][1] aligner. Is alignment stochastic? Can we get (slightly) different alignment from different runs on the same fastq files? [1]: https://github.com/zwdzwd/biscuit ...
biscuit alignment written 10 months ago by irfanwustl0 • updated 6 months ago by zwdzwd120
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Comment: C: cram to bam conversion
... Yes. I am suspecting is it a multithreading issue? ...
written 10 months ago by irfanwustl0
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cram to bam conversion
... I am trying to convert cram file to bam file but I am getting the following error: > [E::cram_get_ref] Failed to populate reference for id 504 > [E::cram_get_ref] Failed to populate reference for id 538 > [E::cram_get_ref] Failed to populate reference for id 608 > ................... ...
genome alignment written 10 months ago by irfanwustl0
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Merging unaligned bam files
... I have two WGBS unaligned bam files (fastq files stored as unaligned bam). I am wondering can I merge those files? Does samtools merge works for unaligned bams? Thanks ...
next-gen written 11 months ago by irfanwustl0

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