User: Shaohua

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Shaohua20
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3 years, 8 months ago
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5 years, 10 months ago
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Posts by Shaohua

<prev • 7 results • page 1 of 1 • next >
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Pindel For Detecting Translocation Events
... Hi KaiYe, I have a question that can Pindel be used to detect inter-chromosomal translocation events? thanks a lot! Shaohua ...
pindel written 3.7 years ago by Shaohua20 • updated 3.6 years ago by Biostar ♦♦ 20
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Comment: C: Filter Reads In The Sam/Bam Files By Direction Using Samtools
... yes, it is quite tricky to estimate the insertion size, for some libraries, the insertion size estimated by bwa is around 3 kb which fits our expectation. However, for some libraries, the range of the insertion size is quite big, from few hundreds bp to 5 kb. This may indicate the mate pair library ...
written 4.4 years ago by Shaohua20
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Comment: C: Filter Reads In The Sam/Bam Files By Direction Using Samtools
... I am not sure what you mean here. I used bwa sampe for the mapping and the results from bwa were first converted by bam format and sorted by default parameters of samtools ...
written 4.4 years ago by Shaohua20
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Comment: C: Filter Reads In The Sam/Bam Files By Direction Using Samtools
... yes, since in principle, the reads in the mate pair library should be <- ->. However, some paired end reads with direction of -> <- were sequenced. For my research, I just want to use the 'true mate pair reads'. I want to filter out those reads are PE reads based on their direction ...
written 4.4 years ago by Shaohua20
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Comment: C: Pindel Segmentation Fault (Version 0.2.4W)
... hi Kaiye, thanks for the suggestion. I saw some people do the reverse complement for the reads of the mate pair library before the mapping step, and then do SV calling using Pindel. I have an another question that how does Pindel handle the paired end read contamination in the mate pair librarie ...
written 4.4 years ago by Shaohua20
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Filter Reads In The Sam/Bam Files By Direction Using Samtools
... Hi all, I am wondering whether there is a way to filter the reads in the sam/bam files by the alignment direction using samtools or other tools? for example, I want to filter out all the reads facing to each other (-> <-) in the mapping result of a mate pair library. Thanks a lot! Shaohua ...
samtools written 4.4 years ago by Shaohua20 • updated 4.4 years ago by Pierre Lindenbaum102k
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Pindel Segmentation Fault (Version 0.2.4W)
... I am using Pindel (version 0.2.4w) to detect SVs for a non-model system. What I have done are: 1st. mapping the mate-pair reads to the reference genome with bwa. 2nd. I converted the sam to bam with samtools and filtered out the reads with mapping quality <20. 3rd. the duplicated reads were ...
pindel written 4.4 years ago by Shaohua20 • updated 4.2 years ago by steve40

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