User: k.rue-albrecht

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Posts by k.rue-albrecht

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Comment: C: The comparison between HISAT2 and Tophat2
... Well, trimming is certainly a bigger deal for DNA-sequencing and variant calling, but there are some questions out there for RNA-seq: - [STAR/tophat2][1] - [paper with tophat2][2] STAR seems to happily align uniquely 83.37% of the trimmed reads (TrimGalore). I am interested in HISAT2 now (for a ...
written 3.1 years ago by k.rue-albrecht20 • updated 11 months ago by RamRS23k
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Comment: C: The comparison between HISAT2 and Tophat2
... Hi, What was the length of your read pairs? Did you read and quality-trim them before alignment? I am testing HISAT2 with SRA files: SRR1303996 and SRR1303997. Prior to alignment, I have used Trim_Galore! to trim adapter and low-quality bases. HISAT returns the following stats: 10116026 read ...
written 3.1 years ago by k.rue-albrecht20
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Answer: A: featureCounts exon counting problem
... Hi, I know I'm a bit late to answer, but I had the same/similar problem, largely answered by Devon's comment: > I wonder if the fact that there are duplicate exon entries is what's causing this. Try adding the -R option and redirect stdout to a file to track how alignments are getting treated. ...
written 3.1 years ago by k.rue-albrecht20
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Answer: A: Haplotype RNA-seq data
... 10 months later... doesn't look like there's much :/ I was actually Googling this question and ended up here. I have just learned about **MMSEQ** (http://bgx.org.uk/software/mmseq.html#note1), but it is based on bowtie, and I am looking for possibly faster alternative (such as STAR or HiSat2) as I ...
written 3.1 years ago by k.rue-albrecht20

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