User: harold.smith.tarheel

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Posts by harold.smith.tarheel

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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 4 days ago by harold.smith.tarheel4.1k
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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 weeks ago by harold.smith.tarheel4.1k
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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 11 weeks ago by harold.smith.tarheel4.1k
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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 12 weeks ago by harold.smith.tarheel4.1k
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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 12 weeks ago by harold.smith.tarheel4.1k
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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 12 weeks ago by harold.smith.tarheel4.1k
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Answer: A: How do we find the number of sequences with terminal mismatches?
... You should be able to obtain that information by parsing the end of the MD tag for three, two, or one 'GATC' characters. The alternative would be to parse the end of the CIGAR string for X characters (mismatch), but I believe Bowtie predates that feature of the SAM standard. ...
written 12 weeks ago by harold.smith.tarheel4.1k
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Comment: C: look for sequences containing a specific motif
... From the user guide: > You can specify whether or not BBDuk looks for the reverse-complement > of the reference sequences as well as the forward sequence with the > flag “rcomp=t” or “rcomp=f”; by default it looks for both. ...
written 3 months ago by harold.smith.tarheel4.1k
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Answer: A: look for sequences containing a specific motif
... An easy method would be to use [BBMap][1]'s kmer counting functionality, plus hamming distance to allow for errors: bbduk.sh in=YOUR.FASTQ outm=MATCHED.FASTQ \ literal=SEARCH_STRING k=STRING_LENGTH hdist=NUMBER_OF_ERRORS [1]: https://sourceforge.net/projects/bbmap/ ...
written 3 months ago by harold.smith.tarheel4.1k
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Answer: A: Gene distribution along the chromosomes
... This [post][1] shows how to bin feature counts by chromosome intervals (substitute gene position file for VCF). Then use R (or even the dreaded Excel) to generate the plot. [1]: https://www.biostars.org/p/218480/ ...
written 3 months ago by harold.smith.tarheel4.1k

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Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
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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
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
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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
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Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
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Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal

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