User: hxlei613

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hxlei61340
Reputation:
40
Status:
New User
Location:
Bangladesh
Last seen:
1 day, 21 hours ago
Joined:
1 year, 4 months ago
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h*******@gmail.com

Posts by hxlei613

<prev • 32 results • page 1 of 4 • next >
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DMAP for RRBS generate blank output
... Hello everyone! Lately I've been using DMAP to analyse my RRBS. Trimming(trim_galore), mapping(bismark) all seem fine. DMAP works well with test data supplied by [DMAP][1]. However when I use my raw bam generated by bismark, DMAP doesn't generate any output and there is no error message.I don't know ...
rrbs dmap written 5 days ago by hxlei61340
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Possible bug for bismark when methylation calling ?
... Hi, I'm using bismark for bs-seq mapping and methylation calling. I take a glance at the coverage file generated by *bismark2bedGraph*. However, the result seems strange. Take CpG site of chrM for example (because chrM is the smallest chromosome). The coverage file contains sites that are not CpG si ...
methylation bs-seq bismark written 4 months ago by hxlei61340 • updated 3 months ago by Santosh Anand500
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Comment: C: Filter a sam file by alignment score.
... AS tag, it means alignment score.I am using bwa( bwa aln and bwa sampe ). ...
written 5 months ago by hxlei61340
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Comment: C: Filter a sam file by alignment score.
... I just want to filter reads with alignment scores less than 1 before subsequent analysis. ...
written 5 months ago by hxlei61340
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Comment: C: Where is the alignment score using bwa-sampe ?
... It seems that AS tag is reported by bwasw and is long-read specific according to [Bio-bwa-help][1]. Can I do filter on alignment score? [1]: https://sourceforge.net/p/bio-bwa/mailman/message/27302622/ ...
written 5 months ago by hxlei61340
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Filter a sam file by alignment score.
... I'm processing pair-end WGBS data following this article : *Single Nucleotide Analysis of Cytosine Methylation by Whole-Genome Shotgun Bisulfite Sequencing*. In brief, read 1 are C to T converted and read 2 are G to A converted.Then the reads were aligned to an in silico converted hg19 to both the ...
alignment score bwa written 5 months ago by hxlei61340 • updated 4 months ago by Biostar ♦♦ 10
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Comment: C: Samtools View: Only Forward Or Reverse Strand
... I also wonder the command for PE reads ...
written 5 months ago by hxlei61340
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Answer: A: Bwa-0.6.1-Tpx.Patch
... What does bwa-0.6.1-tpx (especially tpx) means ? It seems to be the parallel samse/sampe patch from sourceforge.Does this version have big differences from bwa-0.6.1-tpx ? ...
written 5 months ago by hxlei61340
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Answer: A: Bwa Error Using Bwa-0.6.1-Tpx.Patch
... What does bwa-0.6.1-tpx (especially tpx) means ? It seems to be the parallel samse/sampe patch from sourceforge.Does this version have big differences from bwa-0.6.1-tpx ? ...
written 5 months ago by hxlei61340
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Comment: C: Are there any tools able to exclude specific bases (bias) from methylation calli
... I am hesitate to use it because of -D option. Does it mean I need to get exact depth of every base and select the maximum ? The default 2000 may not be suitable for different alignment files. ...
written 5 months ago by hxlei61340

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Popular Question 2 days ago, created a question with more than 1,000 views. For Questions about DAVID
Supporter 5 months ago, voted at least 25 times.

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