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Comment: ATAC-seq troubleshoot - Just Noise
by
ATpoint
76k
Yes, definitely lots of noise and few peaks for such an experiment. Which celltype is that, and which lab protocol did you use?
Comment: DESeq2 analysis using two featureCounts generated from different studies
by
abedkurdi10
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190
What do you mean by gene lists?
Comment: Find potential important genes from bulk-RNA seq experiment
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Michael
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You can use e.g. the WGCNA package for network analysis. In your case multiple samples this might mean multiple patients or a time series o…
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
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Edoardo
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Thank you so much for your responses.
@genomax , I've downloaded both of the databases you recommended. I attempted to combine them into …
Answer: Simulate short-read RNA-seq data from long-read RNA-seq data
by
Mensur Dlakic
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I think you could try doing this, but it wouldn't be appropriate. You'd be bringing long-read errors, which I believe are higher than short…
Comment: Salmon index not progressing
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camillab.
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I opened tow terminals and one was the code to build a decoy-aware transcriptome and the other was building indexes (no decoy)
Comment: Adding a control sample to bulk RNA-seq
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Chris
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Thank you for the explanation! So just want to confirm one control with replicate is totally useless even can't use as a reference?
Answer: DESeq2 analysis using two featureCounts generated from different studies
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swbarnes2
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Comparing samples between labs is a bad idea. Better to generate gene lists from one study from one lab, and gene lists from another study…
Comment: Adding a control sample to bulk RNA-seq
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swbarnes2
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If a sample wasn't prepared along side your treated samples, it is a different batch. If you had treated and controls in each of two diffe…
Comment: kallisto normalized TPM values without bootstraps
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ATpoint
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You don't need sleuth. Typically these deconvolutions, or most downstream analysis, is done on the gene- rather than the transcript-level w…
Comment: Salmon index not progressing
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ATpoint
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If the top $CPU column shows some values in the hundreds then it is doing something (actually when it's > 0%). So based on the screenshot i…
Comment: Salmon index not progressing
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camillab.
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Thank you. Waiting it's not gonna hurt me, when should I stop hoping and give up is the question? do you know is there a way if I can see i…
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Ram
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A more efficient way would be to make a 2 column CSV file, one column with the count value and the other with the chr:start-end range, then…
Answer: Filtering VCF to divide with equal sizes
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avelarbio46
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I divided my contigs using R, but it was more complex than the program Pierre Lindenbaum made (https://jvarkit.readthedocs.io/en/latest/Vcf…
Comment: Salmon index not progressing
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ATpoint
76k
Just wait until it is finished. It's seems to be running. I just checked my logs and on our HPC with four cores such as process for a decoy…
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