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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. …
Comment: interpretartion of a vcf file
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samuelkalandarov2002
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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…
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
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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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Comment: GTF file for Rhinolophus sinicus
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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:
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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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I have 2 files output, no error logs...
the .kreport file: 100.00 160136511 160136511 U 0 unclassified
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agree.
from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
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yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
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