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written 6 months ago by
finswimmer ♦ 11k
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Recent Votes
- General question about batch effect, read trimming and what to do when the adapter trimming step is not working appropriately.
- Too many differentially expressed genes in RNA-seq?
- A: Too many differentially expressed genes in RNA-seq?
- A: Count number of monophyletic groups within pylogeny
- C: Post-filtering WES for mutation calling
- C: Post-filtering WES for mutation calling
- C: Post-filtering WES for mutation calling
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Recent Replies
-
C: General question about batch effect, read trimming and what to do when the adapt by
Mozart • 110
Thanks ATpoint for your question. I am judging the PCA according to someone else's analysis. I h...
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C: How to separate chrY from a WGS vcf file? by
Pierre Lindenbaum ♦ 119k
> If you can't answer, just ignore it. but, as said @jared.andrews07, why don't you look in...
-
C: How to separate chrY from a WGS vcf file? by
krt • 0
Because I have no idea how many snps i should expect from this type of test. I don't know if 649k...
-
A: Count number of monophyletic groups within pylogeny by
jrj.healey ♦ 11k
Here's a fairly simple 'brute force' approach inspired by my previous answer here: https://www.bi...
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C: Mutect2 "somatic" variants with resistant tissue culture lines by
Kevin Blighe ♦ 41k
Indeed, as the population is a 'pure' cell-line, no contamination should be expected. In practice...
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C: Haplotype visualization from postion data by
Kevin Blighe ♦ 41k
Por favor, no puedo ver sus datos - se los puede pegar aquí? Dime lo que significa "*add a colour...
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A: Correlating miRNA count from DeSEQ2 with Transcript FPKM from cuffdiff by
Kevin Blighe ♦ 41k
Your best option may be this: - transform the DESeq2-normalsied counts to variance-stabilised c...
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C: Post-filtering WES for mutation calling by
Kevin Blighe ♦ 41k
Moved to answer. I agree, you should generally leave everything that has aligned until the end, a...
-
C: How to remove batch effects using surrogate variables? by
Kevin Blighe ♦ 41k
26?! ...do you want to eliminate every last bit of useful information from your data? Why do you ...
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C: RNA Seq analysis of rice samples by
Kevin Blighe ♦ 41k
Please show ***all*** commands that you have used. As a community full of volunteers, we do not h...
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C: hisat2 command line fastq to bam by
Adrian Pelin • 2.2k
What happens if you: hisat2 -f -x hg19_indexed -1 reads_R1.fq -2 reads_R2.fq | samtools view...
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C: R analysis for read counts using edgeR by
Liftedkris • 0
i have 24 samples, in three groups, each group consisting of 8 samples 4 each for control and tes...
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