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Recent Replies
Comment: Kraken classified based on 1 mer
by
colindaven
6.7k
Don't always believe sequencer quality scores - here is a nice writeup - https://sequencing.qcfail.com/articles/illumina-2-colour-chemistry…
Answer: Issue understanding ATAC-seq PCA
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LChart
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I know you specified the `--rowCenter` flag in the post - but double-check that you actually specified it when producing the plot. A 95% va…
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> I believe edgeR is used more than DESeq2 for ATACseq, but I'll check to make sure
Their inference is similar, it's a metter of personal …
Comment: Separate single cell BAM file by the cell barcode
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zbidav
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Definitely! I am so sorry for not seeing this on time, I hope this is still relevant.
I will provide the code that works in my case:
…
Comment: Calculation of per-base average Quality (MAPQ, basecall quality Q20) from BAMs a
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Novice
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@genomax Thanks for the depth tools. I will take a look at them. With MAPQ, I want consider all reads that overlap a base to compute averag…
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> Considering the file sizes and the fact that you are using 4 cores normal.
yes
Comment: No available matched normal for Mutect2 GATK
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GenoMax
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> My file sizes are approximately 65 GB each
and
> bwa-mem2 mem step is taking 8+ hours
Considering the file sizes and the fact that you…
Comment: Calculation of per-base average Quality (MAPQ, basecall quality Q20) from BAMs a
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> Normalized depth at every base, across all samples (depth at a base/median autosomal depth).
Use tools like `pandepth` and `mosdepth` to…
Comment: No available matched normal for Mutect2 GATK
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> Also, if the approach is fair, I was also wondering why my bwa-mem2 mem step is taking 8+ hours to run on the C57BL/6J genome
split the…
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It would be best if you marked the tissues with either identical symbols or colors so that you can tell which group is where
The PCA p…
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I recommend using the confidence flag for Kraken2; otherwise, it can generate wildly inconsistent results depending on the input.
Like th…
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DeSeq2 was designed for raw counts data, limma was designed for normalized data, that being said I think both would work, but maybe the lat…
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You are trimming with Illumina adapters rather than polyG,
add the polyG sequence into the adapter fasta file (basically just a bunch o…
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FedeXandeR
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Thank you man for your kind reply. I understand that even few genes (or even one) could, in principle, induce dramatic phenotypic changes, …
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