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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.
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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 :
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#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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After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1])
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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.
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Hmm, okay I'm not sure what is going on, but here is what I did:
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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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I have 2 files output, no error logs...
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