User: irfanwustl
irfanwustl • 0
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Posts by irfanwustl
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... Got it. Yes, the header was not indicated by '#' ...
written 7 weeks ago by
irfanwustl • 0
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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
irfanwustl • 0
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... Sorry for my late response. Actually, I could not resolve it. Is it a bug? ...
written 7 weeks ago by
irfanwustl • 0
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... I am looking for all CpG sites. Is there any bedfile which contains all CpG positions for hg38?
...
written 7 weeks ago by
irfanwustl • 0
• updated
7 weeks ago by
Kevin Blighe ♦ 63k
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... 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 ...
written 8 months ago by
irfanwustl • 0
• updated
7 weeks ago by
Alex Reynolds ♦ 30k
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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
irfanwustl • 0
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... 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 ...
written 10 months ago by
irfanwustl • 0
• updated
6 months ago by
zwdzwd • 120
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Comment:
C: cram to bam conversion
... Yes. I am suspecting is it a multithreading issue? ...
written 10 months ago by
irfanwustl • 0
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5 follow
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... 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
> ................... ...
written 10 months ago by
irfanwustl • 0
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... 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 ...
written 11 months ago by
irfanwustl • 0
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