User: biobiu
biobiu • 10
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Posts by biobiu
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... Hi,
I'm looking for a DNA reads simulator which has the ability to simulate reads with UMIs. Is anyone familiar with such a tool?
thanks in advance ...
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... It really depends on what you are looking for (what is the minimal length of the complementary regions? should they match perfectly? etc.). In example, miRNA should have (almost) exact match in the seed region but does not require any match outside the seed.
Generally speaking, in order to find comp ...
written 16 days ago by
biobiu • 10
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... You may manually check few reads. Align them to both hg19 and hg38 and check the coordinates.... ...
written 4 weeks ago by
biobiu • 10
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... Hi,
Can someone help me understand the re-seeding step in BWA-mem?
I know that BWA-mem works with seeds and exntend approach. It finds the maximal exact match (MEM) and then extending it in both directions.
Can anyone help figure the followings:
1) What happens in the re-seeding step?
2) BWA-mem a ...
written 4 weeks ago by
biobiu • 10
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... Thanks for all responses.
I understand why aligning to the whole genome is recommended.
However, I accepted that most of the reads will still align to the targets when aligning to the whole genome but will be assigned as secondary. It seems that this is not the case here.... ...
written 4 weeks ago by
biobiu • 10
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... I've sequenced targeted DNA panel. I'm aligning it using bwa mem once to the whole genome and twice to the targeted sequences.
When aligning it to the reference genome I'm getting ~30% of the reads mapped to the targeted regions.
However, when aligning it to the panel sequences 70% of the read are ...
written 7 weeks ago by
biobiu • 10
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... Maybe, but since I have to know that my read were mapped correctly I have to filter these cases out. ...
written 14 months ago by
biobiu • 10
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... Thanks. No its before filtering. My problem is not that I have technical problem to filter it out (which can be done easily by awk or grep), my problem is that I'm actually don't understand how it make sense that some reads have MAPQ 0 without XA tag and others have XA with MAPQ greater than 0. So I ...
written 14 months ago by
biobiu • 10
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... For mapping?
bwa-0.7.12/bwa mem -t 16 hg19.bwa_index/hg19 file_1.fastq file_2.fastq > file.sam 2> file.log
Thanks ...
written 14 months ago by
biobiu • 10
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... I'm trying to filter out reads that were primarily aligned to one genomic region (if a read has secondary alignment I want to keep the primary).
I've tried to do this with two methods-
(i) filter out reads with MAPQ=0, which should have been aligned to more than one region.
(ii) read with XA tag whi ...
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