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User: harold.smith.tarheel

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Posts by harold.smith.tarheel

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Answer: A: Find unique non overlapping intervals between two files?
... Use [BEDtools subtract][1] with -A option. [1]: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html?highlight=subtract ...
written 17 days ago by harold.smith.tarheel • 4.2k
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Answer: A: Combining snp and indel vcf files with GATK4
... My guess (easily verified) is that you have some overlapping SNPs and indels that are being merged. I don't know which takes precedence in MergeVcf - v3 CombineVariants allowed the option to specify which one. SortVcf would not resolve overlaps but merely but put them in chromosome/position order, t ...
written 6 weeks ago by harold.smith.tarheel • 4.2k
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Comment: C: how to extract unique variants from GVCF
... @Ram: Sorry for the confusion. I thought your comment was directed at me, since I mentioned cross-posting on GATK. I still intend to share Pierre's solution there, so others will be aware of it. ...
written 3 months ago by harold.smith.tarheel • 4.2k
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Comment: C: how to extract unique variants from GVCF
... Will do. I cross-posted here only b/c the response time there can be... slow. ...
written 3 months ago by harold.smith.tarheel • 4.2k
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Comment: C: how to extract unique variants from GVCF
... As usual, @PierreLindenbaum has the right tool for the job. Thanks! ...
written 3 months ago by harold.smith.tarheel • 4.2k
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how to extract unique variants from GVCF
... [note: cross-posted on GATK forum - still awaiting a response] I have a GVCF (generated using GATK's HaplotypeCaller w/ -ERC GVCF parameter) of 36 related samples and would like to determine the (potentially *de novo*) variants that are unique to each sample. Short of creating 36 N-1 GVCFs for disc ...
gatk variant-calling filtering gvcf written 3 months ago by harold.smith.tarheel • 4.2k • updated 3 months ago by Pierre Lindenbaum ♦ 114k
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Answer: A: why PCA for RNA-Seq but tSNE for scRNA-seq?
... There's a decent non-mathematical description of the relative features of PCA and tSNE (as well as diffusion maps) in this [review][1]. [1]: https://www.sciencedirect.com/science/article/pii/S0098299717300493#bbib66 ...
written 6 months ago by harold.smith.tarheel • 4.2k
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Answer: A: Error in samtools view
... Use GATK: [How to generate an unmapped BAM from FASTQ][1] Use BBMap: [Reformat User Guide][2] EDIT: or use @Pierre's solution. [1]: https://gatkforums.broadinstitute.org/gatk/discussion/6484/how-to-generate-an-unmapped-bam-from-fastq-or-aligned-bam [2]: https://jgi.doe.gov/data-and-tools/bbt ...
written 7 months ago by harold.smith.tarheel • 4.2k
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Answer: A: What cigar to use to count reads with last base mismatch in Rsamtools?
... [How do we find the number of sequences with terminal mismatches?][1] [1]: https://www.biostars.org/p/300596/ ...
written 8 months ago by harold.smith.tarheel • 4.2k
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Comment: C: How do we find the number of sequences with terminal mismatches?
... Bowtie didn't support clipping, only end-to-end alignment (caveat: relying on memory of old software I haven't used in a long time). ...
written 8 months ago by harold.smith.tarheel • 4.2k

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Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 9 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 11 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Appreciated 11 months ago, created a post with more than 5 votes. For C: Do bioinformaticians often break molecular biologists' hearts by being the first
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 14 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Appreciated 14 months ago, created a post with more than 5 votes. For C: Do bioinformaticians often break molecular biologists' hearts by being the first
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Appreciated 15 months ago, created a post with more than 5 votes. For C: Do bioinformaticians often break molecular biologists' hearts by being the first
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Scholar 15 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 15 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 17 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 17 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 17 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 19 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 22 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
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Commentator 23 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
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