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written 10.2 years ago by
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Comment: Use of Kraken output for functional analysis
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gv
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0
Hello,
you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport
cheers,
Answer: To get p-values for the TPM
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sir, deseq2 takes counts as inputs na for the hypothesis testing /to see the variance between the two groups, but in my case what i want is…
Answer: To get p-values for the TPM
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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…
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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. …
Comment: interpretartion of a vcf file
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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])
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by
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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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The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
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There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
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Hmm, okay I'm not sure what is going on, but here is what I did:
1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
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Ok, thank you so much~
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I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
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