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Comment: different FeatureCounts output for the same data
by
GenoMax
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> featureCounts alignment rate is only around 15-20%.
You mean assignment rate? It is that low even after allowing for counting of multi-m…
Comment: alignment result
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GenoMax
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> 20386810 (88.67%) aligned concordantly exactly 1 time
This result is fine.
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Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
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I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM
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dsull
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Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided.
tximport can t…
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gv
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Hello,
you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport
cheers,
Comment: To get p-values for the TPM
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VITALA
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sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM
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dsull
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There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those.
DESeq2 will give you "p values" based on a Wa…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
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dsull
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I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
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In my case , there is only one sample :
here is an example of a some variants generated using minipileup :
#CHROM POS ID REF ALT QUAL FI…
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This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
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A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
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What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
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After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1])
[1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
•
0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome.
[1]: https://www.na…
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