User: godth13teen

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godth13teen40
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Posts by godth13teen

<prev • 36 results • page 1 of 4 • next >
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Extract improperly paired read from BAM file
... Hi, I want to do manual checking on my BAM file after getting the statistic from `samtools flagstat`. I tried to extract the improperly paired read but failed to do so far. I tried to use `awk` to extract read not contain `2` flagstat, but it's not working because the flagstat is bitwise and combin ...
alignment written 13 hours ago by godth13teen40 • updated 11 hours ago by swbarnes28.2k
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Answer: A: How can I call both somatic and germline variants from bam file?
... they are called separately because they serve different purposes. The germline variant only need 1 sample to compare with the reference genome, while the somatic variants only found in tumor tissue, they need to be compared with other normal tissue of the same person. So the answer to your question ...
written 26 days ago by godth13teen40
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Comment: C: Poly-G in head of read NovaSeq
... Yes, I also considered throwing away both the bad reads and their pair. But as I said, this method is just for data processing, not the real cause of the problem ...
written 27 days ago by godth13teen40
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Comment: C: Poly-G in head of read NovaSeq
... I am using TruSeq DNA PCR-Free from Illumina, when I reported the problem, they give me 2 new kits for testing but the problem occurred again ...
written 27 days ago by godth13teen40
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Comment: C: Poly-G in head of read NovaSeq
... I ask Illumina representative but they haven't give me a clear answer yet, unfortunately, they suggest trim the 25G from the read to pass the fastqc, but I disagree with that method, it didn't fix the problem. ...
written 28 days ago by godth13teen40
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Poly-G in head of read NovaSeq
... Hi, I recently got some problems with the output of NovaSeq 6000. I ran sample in paired mode, then found out that a portion of read 2 has poly-G (around 50bp) at the beginning. I understand that NovaSeq is a 2-color system, so the poly-G is likely signal lost, but I don't understand why it only ap ...
sequencing written 28 days ago by godth13teen40
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Estimation of Mapping accuracy when read length decrease
... Hi, I'm currently investigating fastq file from WGS. Sometimes we have low quality read segment, that need to be trimmed to pass FastQC, however I'm afraid that shorter read can lead to higher chance of mismapping, but I don't know how to quantify that. Could you please address me how to calculate t ...
alignment sequencing written 4 weeks ago by godth13teen40
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SNP and CNV combine effect in GWAS
... Hi, I'm studying about the SNP and CNV combine effect in GWAS. Normally, the SNP and CNV are analyzed separately, however, what if there's a SNP on a CNV(Let's call it CNV-SNP)? And what if one chromosome has CNV-SNP, and the other one does not? In the end, we need to encode genetic variants into nu ...
gwas snp cnv written 7 weeks ago by godth13teen40
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Comment: C: Dealing with Multiallelic in GWAS
... Ah, it's clear to me now, thank you ...
written 7 weeks ago by godth13teen40
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Comment: C: Dealing with Multiallelic in GWAS
... Hi, I'm not so clear about your answer, could you please explain a bit more? Thank you ...
written 8 weeks ago by godth13teen40

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