Moderator: swbarnes2

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Posts by swbarnes2

<prev • 779 results • page 2 of 78 • next >
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Answer: A: How does one count unmapped transcripts ?
... I guess you could try to assemble the unmapped reads, and blast the best looking contigs to nr, see if you can identify where they came from. Or just blast the most common unmapped reads. ...
written 11 days ago by swbarnes26.5k
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Answer: A: single cell data analysis
... Why is cellranger's aggr unsuitable for you? ...
written 11 days ago by swbarnes26.5k
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Answer: A: jellyfish kmer counting discrepancy
... From the manual: > In sequencing reads, it is unknown which strands of the DNA is > sequenced. As a consequence, a k-mer or its reverse complement are > essentially equivalent. did you count up the rev-comp of your test sequence too? Also, I'm not totally sure if grep will find every ins ...
written 11 days ago by swbarnes26.5k
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Comment: C: extracting DNA sequnces from multiple fastq.gz files
... Umm, why? Why would you want to do this? ...
written 12 days ago by swbarnes26.5k
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Answer: A: How I deal with raw read counts of RNA-seq
... I'd try "external_gene_name" instead of hgnc symbols. With 25k things having matching names, it looks like hgnc names might only match protein coding genes, but ensembl IDs will include a lot more than that. ...
written 12 days ago by swbarnes26.5k
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Answer: A: Why and how to discard mapped reads based on strandedness?
... I'm not sure most people filter at the bam level, but when you use a program to assign reads to genes, you can tell those programs that your data is stranded, and that it should only count reads aligning in the correct orientation. STAR can be instructed to output the gene counts using all three as ...
written 12 days ago by swbarnes26.5k
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Comment: C: how to extract just one fast sequence from a multiple sequence vcf?
... vcf's typically don't have sequences, are you sure that's what kind of file you've got? ...
written 13 days ago by swbarnes26.5k
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Answer: A: Batch effect and DE using TCGA and my data
... > or DeSeq itself do this when I put batch as design? Yes. Don't try to correct for it, just let DESeq take it into account when making its models. You can also incorporate the design when calculating the PCA plot. ...
written 13 days ago by swbarnes26.5k
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Comment: C: ways to concatenate individual DNA sequences together to form complete sequence
... What tutorials have you looked at? I bolded key words so you would know what to Google. ...
written 16 days ago by swbarnes26.5k
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Comment: C: Why I have too many reads non uniquely aligned?
... > 6 Output in transcript coordinates. With --quantMode TranscriptomeSAM > option STAR will outputs alignments translated into transcript > coordinates in the Aligned.toTranscriptome.out.bam file (in addition > to alignments in genomic coordinates in Aligned.*.sam/bam files). > These t ...
written 17 days ago by swbarnes26.5k

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