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User: harold.smith.tarheel

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Posts by harold.smith.tarheel

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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 21 days 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 21 days 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 21 days 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 24 days ago by harold.smith.tarheel • 4.2k • updated 24 days ago by Pierre Lindenbaum ♦ 111k
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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 3 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 4 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 5 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 5 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?
... I believe 'S' represents soft clipping in the CIGAR. 'X' represents mismatch, but was not used in earlier versions of SAM. ...
written 5 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?
... The MD tag is one of the predefined standards in SAM/BAM file [specification][1], used to represent mismatches. More info can be found [here][2]. EDIT for more information: The MD tag contains the REFERENCE nucleotide at a position if there is a mismatch, so any read that contains a terminal mismat ...
written 5 months ago by harold.smith.tarheel • 4.2k

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Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
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
Scholar 6 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 8 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 8 months ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Appreciated 8 months ago, created a post with more than 5 votes. For C: Do bioinformaticians often break molecular biologists' hearts by being the first
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
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
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
Appreciated 12 months ago, created a post with more than 5 votes. For C: Do bioinformaticians often break molecular biologists' hearts by being the first
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Scholar 12 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 12 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 12 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
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
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
Scholar 16 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 18 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
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
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
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